Lewandowski received 356 of the 563 votes cast in the poll carried out by sports magazine Kicker among sports journalists.
The goal-getter won competition from fellow teammates Thomas Muller and Joshua Kimmich as well as Dortmund's Erling Haaland.
In receiving the award in Saturday's fixture against Hertha Berlin, the 33-year-old said;
"I know what a great honour this is.
"It's a source of great pride and joy for me, because it's rare for someone to win the title of Footballer of the Year in Germany twice in a row."
The former Borussia Dortmund forward won the vote in July but has now been officially honoured.
Having broken Gerd Muller's long-standing record in the Bundesliga with 41 goals last term, there was never going to be any strong competition against the Pole for the award.
Lewandowski helped Bayern Munich to a Champions League truimph in the 2019-20 season but failed to defend the accolade the following year.
The bulky striker has worked with a host of wingers and after the departure of perfect duo Franck Ribery and Arjen Robben, Lewandowski in a recent interview insisted he understands the complexities of working with different wingers.
"It changes the dynamic in attack but you simply have to learn how to read your team-mates and anticipate their movements.
“Some wingers are more interested in scoring themselves than others but that doesn’t mean you won’t get chances: if they shoot more often, there’ll be more loose balls off the goalkeeper or defenders that you can take advantage of. You just have to be one step ahead.”
