كتب : Amro Hssan
The 21-year-old midfielder scored his second of the game on 90 minutes to grab a valuable draw for Markus Babbel's team.
Khedira was the one to break the game's deadlock on 45 minutes, before Tim Borowski leveled for the visitors.
In the second half, Bayern added a second through Luca Toni in the 66th minute.
The Bavarians had to complete the game with ten men after Italian right-back Massimo Oddo was sent off in the 85th minute.
Stuttgart took full advantage as Khedira equalized in the game's last minute.
The draw lifts Bayern temporarily to the Bundesliga summit with 35 points prior to Hoffenheim's clash with Schalke on Sunday. Stuttgart are tenth on 25 points.
In other games, Hertha Berlin thrashed Karlsruhe 4-0 at the Olympic stadium and HSV Hamburg scraped a hard fought 1-0 over Eintracht Frankfurt.