They held on for a 4-2 victory despite conceding twice in the final 10 minutes. Goals from Nick Woltemade, Enzo Millot and Deniz Undav had Stuttgart three up inside 28 minutes and cruising against Bielefeld, just the fourth third division side to make the final in the competition's 82-year history.
Millot added a second with 66 minutes and Stuttgart looked to have the job done, but a Julian Kania strike and a Josha Vagnoman own goal with the clock ticking down made Stuttgart sweat.
They however held on to claim their fourth German Cup and their first since 1997, when the then Joachim Loew-coached side again triumphed against third-flight opponents Energie Cottbus.
"I'm completely exhausted. The emotions are running high. I can't even put it into words," Stuttgart defender Maximilian Mittelstaedt, who was born and raised in Berlin, told TV network ZDF.