Robert Lewandowski put the champions into an early lead at the Allianz Arena, but Naldo thumped in a free-kick four minutes later and Schalke had the better of the chances until a late flurry of goalmouth action as Bayern grew more and more desperate.
But a season in which Ancelotti has struggled to get the best out of his squad lurched to another disappointment on Saturday as the leaders ground out another disappointing result.
"It was a tough game for us, Schalke played well," the Italian said. "We started well, but then we were not compact enough.
"The defensive and midfield lines were not close enough together. We did not win the important balls, so we had problems.
"Overall, it was not enough, now we are focusing on the next game."