The Spaniard led his side to victory Friday but paid tribute to the club's former coach for making the achievement possible.
Chelsea led twice on the night, with Fernando Torres making it 1-0 before Franck Ribery leveled to take the game into extra time. The Blues again took the lead, this time through Eden Hazard, but then saw Ramires sent off for a second yellow card, with Bayern leaving it late to pull level as Javi Martinez's last-gasp strike ensured a penalty shootout.
David Alaba, Toni Kroos, Philipp Lahm, Franck Ribery and Xherdan Shaqiri all converted their spot kicks, while Manuel Neuer saved one from Romelu Lukaku, to hand Bayern the trophy.
Guardiola said: "Heynckes is the architect and creator of this title. I want to dedicate it to him."
Heynckes guided Bayern to the treble last year, but the club opted to appoint Guardiola his successor before the end of last season, with the Spaniard unattached after embarking on a yearlong footballing sabbatical upon leaving Barcelona.
The 42-year-old has guided Bayern to three wins and a draw in its opening four Bundesliga games but lost the DFL-Super Cup to Borussia Dortmund.