The second half saw no let-up from the Bundesliga leaders. Nicolas Jackson added a fourth early in the period, calmly slotting home after being played through by Luis Diaz.
Olise then secured his brace with another sensational left-footed strike following a surging run from the unfortunate Davies. Jamal Musiala, introduced at the break, completed the rout in the 67th minute by tapping home a low cross from Jackson.
The sixth goal further highlighted the chasm in quality between the two sides, as the Italian outfit struggled to cope with the relentless movement of Bayern's attacking quartet.
In the final moments of the encounter, Atalanta managed to find a late consolation. Mario Pašalic stepped up in stoppage time to score a lone goal for the visitors, though it did little to dampen the dominant display from the home side.