The 28-year-old beat off competitions from the likes of Kamil Glik, Grzegorz Krychowiak, Arkadiusz Milik and Michal Pazdan to lift the trophy once more.
"I am delighted that I have again managed to win the award for the player of the year," the striker commented.
"The award means a lot to me and it is a great honour."
Lewandowski enjoyed a hugely successful 2016 on club level as Bayern won the domestic double, with the prolific attacker playing a key role in their successes as he was crowned Bundesliga top scorer.
He scored once in five appearances at Euro 2016 as Poland made it to the quarter-finals, where eventual winners Portugal proved to be too strong after penalties.