Heading into their first match following the mid-season break, Pep Guardiola's defending champions were unbeaten in the league and had only conceded four goals.
The tally was ultimately doubled on a remarkable evening at the Volkswagen Arena as Bas Dost and Kevin de Bruyne scored two goals apiece and second-placed Wolfsburg closed the gap at the summit to eight points.
Juan Bernat netted when Bayern were 3-0 down but his strike could not prompt a comeback as Boateng and his defensive colleagues continued to struggle under a relentless attacking display from Dieter Hecking’s team.
"It's simple – we played really badly," Boateng told reporters, as quoted on his club's official website.
"It might be good that it's happened to us today because it's a wake-up call. We can't afford another performance like that.
"We weren't aggressive and gave away possession far too easily. We have to take a good, long look at ourselves.
"We all know we'll need a vast improvement against Schalke if we're to make amends for this."
Dost opened the scoring on the counter-attack after four minutes and both De Bruyne's goals came as direct passes from Maximilian Arnold easily unpicked Bayern's backline.
"It wasn’t our day," said captain Bastian Schweinsteiger. "We often lost our shape when we attacked and they picked us apart relatively easily on the break.
"That shouldn't be happening. We need to work out what went wrong and do better in our next match."
Guardiola offered praise to Wolfsburg's display on an emotional evening when the club and their fans paid tribute to 20-year-old midfielder Junior Malanda, who tragically died in a car crash earlier this month.
"Wolfsburg were better and scored their goals at just the right time - congratulations," Guardiola said. "We need to analyse what's happened and focus on the next game."
