Youssef El Arabi caught Manuel Neuer off guard in the 23rd minute with a powerful downward header that pushed the Germany goalkeeper behind the goal line.
But the heavily marked Lewandowski found space 11 minutes later to fire in a loose ball after a shot from Thomas Mueller was blocked by Jose Sa. The Poland striker added the second two minutes after the hour mark, swinging his leg high to tap past Sa.
Substitute Corentin Tolisso made it 3-1 with a stylish shot from outside the area in the 75th. Olympiakos hit back four minutes later through Guilherme, with a deflection helping his volley beat Neuer.
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Bayern leads Group B with nine points after routing Red Star 3-0 and Tottenham 7-2 in their previous matches.
Tottenham thrashed Red Star in the group’s other game on Tuesday.