The Stuttgart shot-stopper produced two wonderful saves to deny Thiago but was helpless to deny the Spaniard's sublime scissorkick in injury time.
The centre-back produced a number of brilliant interceptions to frustrate the Bayern attack in the first half although he found life more difficult with Mandzukic's introduction.
The Japanese right-back helped to restrict the attacking threat of Alaba and it was no surprise that Bayern got more into the game after his withdrawal through injury.
The 20-year-old used his strength and athleticism to keep Gotze quiet and he was extremely unfortunate to be on the losing side.
A brilliant display from Rausch who read play excellently to prevent attacks down the Bayern right. Also offered a good outlet on the overlap.
Despite his tender years, he showed grit and determination to close down the Bayern midfield. Looks to be following in his brother's footsteps.
The on-loan Dortmund man was tidy in possession and his effective pressing game restricted the impact of Kroos in midfield.
The 17-year-old looks destined for a bright future after a confident display down the left. He was instrumental in the opening goal, although he often lacked composure in key areas and spurned several good chances.
He ran his socks off up front and although he did not have a major impact on the game, his work rate set the tone for his team's display. Claimed the assist for Ibisevic's goal.
The Austrian enjoyed a fine first-half display and often got the better of his international colleague, Alaba, down the right. Was at the heart of most of Stuttgart's attacks.
The Bosnian scored his 10th league goal of the season with a composed finish inside the box. His impressive work rate helped to limit Bayern's space.
He controlled his area effectively and made a few routine stops to deny the Stuttgart attack. However, he could do nothing to prevent Ibisevic's opener.
The Brazilian performed the sweeper role to perfection and made a crucial sliding challenge to prevent his side going behind late on. Lost his temper midway through the game which meant he lost his concentration.
Was given a tough time by Ibisevic, particularly in the first half. However, on the whole, he performed his defensive duties well and proved insurmountable in the air.
He was fortunate not to see a penalty awarded against him for handball and will be disappointed by the quality of his final ball in the final third. However, he did produce the cross for Thiago's stunning winner.
The Austrian was often exposed down the wing by his willingness to gallop forward and assist the attack. Struggled to merge a good link with Shaqiri.
The Bayern captain was slick in possession and helped his side to get back into the game with his ability to retrieve the ball and spring attacks.
Not his finest display in the Bayern jersey. Tested the Stuttgart defence with a number of intelligent runs but he did not always receive the service he desired.
A disappointing display from Kroos who failed to influence proceedings in midfield. Summed up his performance by throwing his gloves at the bench when substituted.
The Swiss winger struggled to get into wide positions and looked lightweight in possession. However, he often found pockets of space behind the Stuttgart defence and came close to scoring on two occasions.
A wonderful performance from the Spaniard who was the creative hub for the majority of Bayern's attacks. It was not surprising that he proved to be the matchwinner as he wrapped up the points with a stunning scissor-kick.
He always looked dangerous with his instinctive movement and eye for goal. However, he often failed to pick out a team-mate in the final third.
The Croatian was keen to impress after being left out of the last game for his poor attitude in training. He gave Bayern a more direct route to goal and his presence caused the Stuttgart centre-backs problems.
The Chile veteran showed he has still got it as he rescued Bayern when they most needed it, ghosting into the box to glance a header beyond Ulreich.