The veteran 32-year-old Cameroon striker, understudy to this season's Bundesliga top scorer Robert Lewandowski, was out of contract this month but has signed a new deal until 2023.
Choupo-Moting scored nine goals in 32 matches for Bayern last season in all competitions and helped the Bavarian giants win a ninth straight Bundesliga league title.
When Lewandowski was sidelined by a knee injury in April, Choupo-Moting scored against his former club Paris Saint-Germain in both legs of the Champions League quarter-final as Bayern bowed out on away goals.
"I am proud to be here. FC Bayern is a very special club, the number one club in Germany and also one of the best clubs in the world," said Choupo-Moting in a statement. "I want to continue to have success with the team, I'd like to reach the German Cup final in Berlin and ideally win the Champions League."
Bayern sports director Hasan Salihamidzic described Choupo-Moting as a "a very important player for us, who performed strongly last season" and who can "help us achieve our goals in the next two years".
Bayern are set to start the 2021/22 Bundesliga season with Oliver Kahn as the club's new chairman and Julian Nagelsmann as head coach, replacing Hansi Flick who will take charge of the Germany team after the Euro 2020 finals.