With top spot in Group A already ensured for the holders heading into the encounter in Munich, Hansi Flick's side had little pressure on their shoulders.
A toothless first-half display paved the way for a much-improved performance after the break as Niklas Sule's towering header and an excellent finish from Eric Maxim Choupo-Moting saw Bayern return to winning ways after drawing with Atletico Madrid last week.
Flick has now won 13 of his 14 Champions League matches in charge of Bayern, who have shown little let up following their triumphant campaign last term.
Bayern enjoyed 69.