As noted above, Model had arrived at the conclusion, based on previous experience, that having reached their first major objective, the Soviets would pause for several days, in order to resupply and regroup, as they had advanced 125 miles (200 km), which was greater than their usual limit on one issue of supplies. Model was wholly mistaken in reaching this conclusion, for while the Soviets had indeed reached their first major objective, the Stavka had ordered that the offensive be carried farther to the west on a broad front without pause. General Hovhannes Kh. Bagramyan’s 1^st Baltic Front was to advance toward Dvinsk, General Ivan D. Chernyakovsky’s 3^rd Belorussian Front was to press forward to Molodechno and thence via Vilnyus and Lida to the Niemen river, and General Konstantin K. Rokossovsky’s 1^st Belorussian Front was to drive forward to Baranovichi and thence to the west toward Brest-Litovsk. General Polkovnik Georgi F. Zakharov’s 2d Belorussian Front was to remain where it was and mop up the encircled German forces in the area of Minsk.

Chernyakhovsky ordered that his main mobile exploitation forces, namely the 5^th Guards Tank Army and General Leytenant Nikolai S. Oslikovsky’s III Guards Cavalry Corps, press ahead with their advance from Minsk on 5 July in the direction of Vilnyus, with the object of reaching the city by the following day: these formations were to encircle Vilnyus from the south and north respectively. The infantry divisions of General Leytenant (from 15 July General Polkovnik) Nikolai I. Krylov’s 5^th Army were ordered to follow in the mobile formations' wake and close with them as swiftly as possible. To the south, General Leytenant Ivan I. Lyudnikov’s 39^th Army was ordered to advance toward Lida, and General Polkovnik Kuzma N. Galitsky’s 11^th Guards Army was to press forward on the front’s centre.

As the Soviets launched their Vilnyus operation, the German forces comprised the southern flank of Reinhardt’s 3^rd Panzerarmee in the form of General Gerhard Matzky’s XXVI Corps, Generalmajor Rainer Stahel’s garrison of Vilnyus, and the remnants of the 4^th Army in the form of von Saucken’s XXXIX Panzerkorps, Generalmajor Helmuth Weidling’s Sperrgruppe 'Weidling') and Generalleutnant Theodor Tolsdorff’s 340^th Volksgrenadierdivision. The Soviet forces comprised Chernyakhovsky’s 3^rd Belorussian Front with General Leytenant Kuzma N. Galitsky’s 11^th Guards Army, General Leytenant Nikolai I. Krylov’s 5^th Army, General Leytenant Vasili D. Kryuchenkin’s 33^rd Army, General Leytenant Nikolai Ye. Berzarin’s (later General Leytenant Ivan I. Lyudnikov’s) 39^th Army, General Leytenant Vasili V. Glagolev’s (later General Leytenant Piotr G. Shafranov’s) 31^st Army and Rotmistrov’s 5^th Guards Tank Army, all supported by General Polkovnik Timofei T. Khryukin’s 1^st Air Army.

Soviet reports suggested that their northern-flank formations advanced to schedule, though noting that there was some resistance from scattered remnants of the destroyed VI Corps (commanded by General George Pfeiffer until his death in an air attack on 28 June) of the 3^rd Panzerarmee, but stated that the 11^th Guards Army in particular encountered strong German resistance and was on several occasions counterattacked. The 5^th Panzerdivision was unable to hold Molodechno, however, and the 5^th Army was able to advance to the outskirts of Vilnyus by 8 July, while the 5^th Guards Tank Army encircled the city from the south, thereby trapping the garrison. Another significant rail junction, Lida was captured by the III Guards Cavalry Corps on the evening of 8 July after the German defenders, who were for the most part low-grade but infamously brutal Waffen-SS units of SS-Obergruppenführer und Generalleutnant der Waffen-SS Curt von Gottberg’s Kampfgruppe 'von Gottberg' and SS-Brigadeführer und Generalmajor der Waffen-SS Bronislav Kaminski’s Waffen-Sturmbrigade 'RONA' abandoned their positions in trench lines dating from World War I, despite reinforcement by the Sperrgruppe 'Weidling', which abandoned its attempt to hold Vilnyus on 9 July.

In overall terms, the Soviets had driven forward altogether more rapidly than Heeresgruppe 'Mitte' could deploy its inadequate forces even to attempt a stand. Thus Soviet troops had passed through the 'narrows' to the south and east of Molodechno by 6 July, and the 3^rd Belorussian Front reported that it now possessed total freedom of movement toward Vilnyus. Generaloberst Walter Weiss’s 2^nd Army managed to commit sufficient formations around Baranovichi to check the Soviet advance for a few days, but one Panzer division and one Hungarian cavalry division could in no way bring to a halt four Soviet tank corps backed by infantry. Baranovichi fell to the Soviets on 8 July, as did Lida, the road and rail junction to the west of the Nalibocka forest.

By stretching its front to the west, Heeresgruppe 'Nord' had been able to reduce the gap to the 3^rd Panzerarmee to some 20 miles (32 km). Friessner was planning an attack to the south with three divisions, but the 1^st Baltic Front’s 4^th Shock Army and 6^th Guards Army started to press toward Dvinsk and thus tied down everything on the army group’s flank. Friessner then proposed as a 'small solution' that General Paul Laux’s 16^th Army could withdraw to the 'Litauen-Linie', which was being rapidly improvised between Kraslava (to the east of Dvinsk) and Ostrov, but Hitler refused to countenance a withdrawal of anything more than half of this distance.

During the battle for the city of Vilnyus, Krylov’s 5^th Army and Rotmistrov’s 5^th Guards Tank Army engaged the German garrison of the Festung 'Vilnyus' (399^th Grenadierregiment and 240^th Artillerieregiment of Generalleutnant Siegfried Hass’s 170^th Division, 1067^th Grenadierregiment, one battalion of the 16^th Fallschirmjägerregiment, the anti-tank battalion of Generalleutnant Albrecht Wüstenhagen’s 256^th Division and a miscellany of other units) under the command of Stahel, who was a Luftwaffe officer. The 35^th Guards Tank Brigade initially took the airfield, defended by the paratrooper battalion, and then there began bitter street-by-street fighting as the Soviet forces battled to reduce the defence.

On 12 July the garrison’s parent formation, namely the 3^rd Panzerarmee, launched a counterattack. Generalleutnant Rudolf Freiherr von Waldenfels’s 6^th Panzerdivision, organised into Major Walter Pössl’s Kampfgruppe 'Pössl' and Major Dr Paul Stahl’s Kampfgruppe 'Stahl', attacked to the east from outside the encirclement: Reinhardt and Waldenfels personally accompanied the advance group. The opposing Soviet forces, taken by surprise and hampered by extended lines of supply, were not able to hold the cordon and some of the 6^th Panzerdivision's units were able to advance some 31 miles (50 km) to link with forward elements of the Vilnyus garrison.

There followed a fierce battle on the banks of the Neris river as men of the Polish Home Army sought, without success, to stop the relief force. In the city itself, a Soviet attack on the morning of 13 July managed to split the German forces into two pockets centred around the prison and the observatory, but some 3,000 Germans escaped through the corridor opened by the 6^th Panzerdivision before Soviet forces closed the gap. Even so, something in the order of 13,000 German troops were lost (8,000 killed and 5,000 taken prisoner according to Soviet estimates) as the city was finally captured toward the evening of 13 July.

Despite the Soviet forces' success, Rotmistrov’s commitment of a tank corps in costly urban fighting combined with earlier disagreements with Chernyakhovsky resulted in his replacement as commander of 5^th Guards Tank Army by General Polkovnik Vasili T. Vosky.

While the Germans did not succeed in their aim of holding Vilnyus as a Festung (fortress), their sturdy defence helped to stop the Soviet forces' drive to the west for a few days: most importantly, it tied down the 5^th Guards Tank Army, which had been instrumental in the initial successes of the Soviet forces in 'Bagration'. This delay gave German forces a chance to re-establish something resembling a continuous defence line farther to the west, although this new continuous front line could be held for only a short time. Without the traffic network dependent on Vilnyus, the German position in the southern part of the Baltic states was no longer tenable. By the end of July, the 3^rd Belorussian Front was ordered to conduct the 'Kaunas Offensive Operation' and so further extend the gains made in 'Bagration'.