Bayern returned to Munich in low spirits following their disappointing trip to England, where they fell to a 3-1 defeat to Arsenal in the UEFA Champions League.
Their mood was certainly not helped by a poor start to proceedings against relegation-threatened St. Pauli, who netted a surprise sixth-minute opener at the Allianz Arena.
After stealing possession off Joshua Kimmich, Mathias Pereira Lage played a neat ball through for Andréas Hountondji to race into the box and fire a low shot past Manuel Neuer at the near post, not long before he was forced off through injury.
Bayern quickly set about levelling the scoreline as Lennart Karl curled a left-foot shot against the far post, before Tom Bischof saw his deflected effort bounce off the upright.
After surviving those scares, the visitors looked set to scrape through to the break until their luck eventually ran out on the stroke of half time.
Luis Díaz received the ball in the box, and despite stumbling to the ground, he had the wherewithal to backheel it for Raphaël Guerreiro to drill home.
With the momentum in their favour, there may have been an expectation that Vincent Kompany’s side would make a fast start and hit the front in the opening stages of the second period.
However, to St. Pauli’s credit, they did their utmost to spoil the home side’s attacking efforts. The woodwork also frustrated the hosts as Harry Kane rattled a fierce strike against the far post after pouncing on Nikola Vasilj’s unconvincing punch from a corner.
Bayern appeared to have run out of ideas until Díaz broke St. Pauli’s hearts in the 93rd minute. The former Liverpool forward found the space in the visitors’ weary backline to head in from Kimmich’s inviting delivery.
There was still time left for Nicolas Jackson to seal the deal with a composed finish to send the hosts eight points clear at the top and leave Alexander Blessin’s side one point adrift from safety.
Flashscore Man of the Match: Luis Díaz (Bayern Munich)