Having claimed a record 41 Bundesliga goals last season, Lewandowski has picked up where he left off last term.
The Poland striker is among the favourites to win the Ballon d’Or on November 29 having been named FIFA’s best male player of 2020.
Lewandowski scored with a stunning striker after Serge Gnabry gave hosts Bayern a first-half lead.
Replacements Eric Maxim Choupo-Moting and Kingsley Coman grabbed late goals to seal the win which keeps Bayern a point clear at the top of the table ahead of Borussia Dortmund, who won 3-1 at Arminia Bielefeld.