Heynckes led Bayern to a Bundesliga, DFB-Pokal and Champions League treble, the first of its kind for a German club, while the Bavarians also had the best disciplinary record in the division last term.
They received just 35 yellow cards in 34 games with only one red card, as the result of a second booking.
"Jupp Heynckes is not only an excellent coach, but he is also an extraordinary person who stands for the values of respect and fair play," said DFB president Wolfgang Niersbach.
"Last season, he showed in an impressive way that success and fair play go hand in hand for him.
"Bayern not only won the treble, but they were also the fairest team last season. Football needs role models like Jupp Heynckes."
Heynckes, who left Bayern at the end of the season with Pep Guardiola taking over the helm, will pick up his award at an event prior to Germany's World Cup qualifier against Austria in Munich on Friday night.
"Fair play is as much a part of football as the rules of the game," said the 68-year-old.
"The different characters within a side have all got to fit in together, and that requires a structure which consists of discipline and fair play."