The 68-year-old leaves the Allianz Arena with his name firmly etched in the record books and will announce his next move in the coming days.
Goals from Thomas Muller and Mario Gomez enabled die Roten to survive a late scare as their cup opponents pulled two back on Saturday, allowing Heynckes to hoist his third trophy at the end of a remarkable season.
"This is an emotional moment. I'll give a final press conference this Tuesday, then I'll say something about my future, whether I'll continue or not," Heynckes told Sky after the match.
"The team gave me the best possible present today. This treble is unique. The decisive factor was the team spirit. Everyone stood together to support each other."
Sports director Mathias Sammer weighed in with his compliments of the coach's triumph.
"Heynckes is now getting the recognition he deserves," Sammer said. "He has a distinguished clarity in terms of planning, meticulousness, diligence and wisdom."
And FCB CEO Karl-Heinze Rummenigge was on hand to conclude: "Heynckes has done a great job and delivered a magnificent season. Even the great team of the '70s didn't achieve the treble."