The prolific Polish international started and scored for Hansi Flick's side during a comfortable 3-0 first-leg victory at Stamford Bridge on Tuesday night.
However, he looks set to be sidelined for the return fixture against Chelsea at Allianz Arena on March 18 after being ruled out for four weeks as the result of a "fracture of the tibia at his left knee joint".
Bayern said: "After 10 days of being immobilised in plaster, build-up training will begin. The total downtime will be around four weeks."
Such a time frame would also see Lewandowski sit out Bundesliga meetings with Hoffenheim, Augsburg, Union Berlin and Eintract Frankfurt, with reigning champions Bayern currently sitting just a point ahead of title rivals RB Leipzig at the summit as they go in search of an eighth consecutive domestic title.
The Polish national team - with whom Lewandowski serves as captain - also play friendly matches against Finland and Ukraine at the end of March as they continue preparations for Euro 2020.
Lewandowski has been in typically red-hot form so far in 2019-20, netting 36 times for Bayern across all competitions, including 25 in the Bundesliga.