Lewandowski was at the Champions League group draw in Geneva to receive the award, just weeks after Bayern won the 2019/20 edition of the competition.
The Poland striker scored 55 goals in 47 games as Bayern also won the Bundesliga and German Cup.
“It’s an amazing feeling, because you work so hard, so this trophy is something special,” said Lewandowski after receiving the award.
“I have to say thank you to my team-mates and coaches who helped me get where I am. Also, my family have given me so much support and are so important.”
Lewandowski also picked up the award for best forward in last season’s Champions League after amassing 15 goals in 10 games. In one match against Red Star Belgrade he needed just 14 minutes to score four times.
The 32-year-old was also top scorer in the Bundesliga last season with 34 goals, equal to a goal a game in the 18-team league.
It was the fifth time he claimed the ‘cannon’ award for the highest number of goals in the German top flight since arriving at Bayern from Borussia Dortmund in 2014.
Lewandowski would have been the strong favourite to win this year’s Ballon d’Or had it not been cancelled by France Football magazine due to the coronavirus pandemic.