Bayern’s Alphonso Davies was sent off after 12 minutes only for Lewandowski to open the scoring five minutes later.
Serge Gnabry doubled Bayern’s advantage and Lewandowski completed his hat-trick with two further goals before half-time.
The Poland striker has now scored 42 times for Bayern this season.
With referee Daniel Schlager showing Davies a straight red for a foul on Stuttgart’s Wataru Endo, Bayern’s winning run – which stood at five going into Saturday’s game – initially looked in danger.
However, three goals in the following 11 minutes put the game beyond doubt and the hosts cantered to all three points after the restart.