The 68-year-old ended a 48-year career in the sport by guiding Bayern to the Bundesliga, German Cup and Champions League titles.
"It means a lot to pick up an award right at the end of my career," Heynckes said at the awards ceremony. "Normally in team sport it is often difficult to put things together like this.
"It isn't just down to me, this is down to the whole club, Bayern Munich, everybody that has been working with me during this period."
He won the award ahead of former Manchester United manager Alex Ferguson and fellow German Juergen Klopp, coach of Borussia Dortmund.
Heynckes began as a player with Borussia Moenchengladbach in 1965 and spent his entire career there, apart from a three-season spell at Hanover 96.
As a coach he led Moenchengladbach, Athletic Bilbao, Eintracht Frankfurt, Tenerife, Real Madrid, Benfica and Bayer Leverkusen, as well as three stints with Bayern.