The all-conquering Bavarians, who had previously landed the Bundesliga and Champions League titles, led 3-0 before Stuttgart struck twice in a 10-minute spell and almost grabbed a stoppage-time equaliser.
Bayern, runners-up in all three competitions last season, were cruising when a harsh penalty converted by Thomas Muller and two Mario Gomez goals against his old club put them 3-0 up inside 61 minutes.
Stuttgart, hammered 6-1 by the Bavarians in the Bundesliga, then gave the European champions a real scare as Martin Harnik pulled two goals back and Bayern goalkeeper Manuel Neuer stopped Serdar Tasci's header on the line with almost the last touch of the game.
Heynckes has left the Spaniard with a tough act to follow as he has managed to rotate the team and keep Bayern's wealth of international players happy even when they have been dispatched to the bench.
It was Bayern's ninth league and cup double and the 15th time they have won the cup competition.
"It's unbelievable what the team has achieved this season," captain Philipp Lahm told ARD television.
"Heynckes has got the recognition he deserves," said sporting director Matthias Sammer. "He has distinguished himself by his clarity, planning, attention to detail, diligence and wisdom."
Just as in last week's 2-1 Champions League final win over Borussia Dortmund, Neuer prevented Bayern falling behind with some outstanding stops.
Stuttgart nearly took an early lead when Alexandru Maxim hooked Ibrahima Traore's swerving cross just wide of the post from 12 metres.
They went two ahead in the 48th minute when Lahm's low cross was scrambled into an empty net by Gomez.
Gomez's second goal in the 61st minute was far more convincing
