After leading Bayern Munich to an unprecedented treble in 2013, the club's former boss beat out Jurgen Klopp and Sir Alex Ferguson for the prestigious award.
Heynckes led the Bavarian club to an unprecedented treble during season 2012-13 before making way for Pep Guardiola in the summer.
Having picked up the award, Heynckes was quick to pay tribute to the staff who helped him during his third and final spell in Munich.
"I’m tremendously thankful to be here to pick up this award today," he said. "It means an awful lot to me to pick up an award at the end of the career. It’s not down to me. It’s down to the whole of Bayern Munich, everybody that’s concerned from the president to the players.
"They produced amazing performances and the coaching staff have made contributions. I want to thank everybody who has pulled together and helped me produce this winning team."
Heynckes' Champions League medal, picked up with a 2-1 win over Borussia Dortmund at Wembley in May, was the second of his career, having previously won the competition in 1998 with Real Madrid.