Andries Jonker's men have to settle for third place, and only a spot in the qualifiers, after coming from behind to claim victory on the final day of the Bundesliga
Bastian Schweinsteiger popped up with the winner in the second half to secure the three points, but that was not enough for Bayern to claim second place as Bayer Leverkusen will enter the Champions League directly instead after their 2-1 win at Freiburg.
The hosts made their intentions known right from the start, pressuring Stuttgart all over the pitch, looking for opportunities to exploit. Miroslav Klose sent two warning shots before the 10-minute mark as the hosts pushed for the opener.
The striker recorded the miss of the season moments later when he failed to find the open goal from three yards out after some stunning work by Arjen Robben down the flank. The fans watched in disbelief as the ball flew over the bar and into the stands.
Bayern continued to press, but their play was lacking the dynamic edge from the games against St Pauli and Schalke. Stuttgart were growing in confidence and were looking increasingly dangerous on the counter.
Okazaki popped up with the opener out of nowhere in the 24th minute as he tapped a Martin Harnik cross at the left post after racing ahead of Philipp Lahm to give the Swabians the lead. Stuttgart's rise continued and moments later Christian Trasch forced Hans-Jorg Butt into a fine safe with a dipping finish from the left wing.
It was the usual suspects who would have the next say in the scoreline as Bayern equalised in the 37th minute. Robben exquisitely threaded a defence-splitting pass for Gomez, who confidently poked the ball between Sven Ulreich's legs.
Pavel Pogrebnyak was presented with a great chance moments before half-time, but was denied by Butt for what proved to be the final moment of interest for the first period.
Top Gun | Mario Gomez finishes the season as top goalscorerBayern Munich went out all guns blazing after the break and laid siege to Stuttgart's goal. Muller failed to connect on two occasions with crosses from Schweinsteiger in the following minutes as the hosts tightened their grip.
It took a header from Schweinsteiger to break Stuttgart's resilient defence as the Bavarians finally went in front in the 71st minute. Toni Kroos sent in a very good delivery from a corner on the left, and with Ulreich off his line, Bayern's vice-captain made no mistake from seven yards out.
Near the 80 minute mark, Gomez hit the bar with an unorthodox finish following a cross by Muller. Both teams had a few decent chances before the full-time whistle, but there were no more goals in this game as Bayern finished third in the standings, and Stuttgart 11th.