Bayern grabbed the lead on 31 minutes when defender Holger Badstuber sent a free kick into the box and Daniel van Buyten was at hand to tap in after Schalke's Kevin Kuranyi accidentally headed the ball into the Belgian's path.
The balance was restored just before the break when Lukas Schmitz floated a free kick into the box and Matip, until recently in Schalke's under-19 team, rose above Bayern defenders to head home.
Leaders Bayer Leverkusen are on 26 points following Friday's 4-0 win against Eintracht Frankfurt, while Werder Bremen in second on 22 points, as many as Schalke, take on Borussia Dortmund on Sunday.
Bayern drop to eighth on 20 points.
"I am satisfied with our performance," Schalke coach Felix Magath told reporters. "I am a bit sad that we did not dare to do a bit more after our good start and ended up reacting more."
Schalke were the hungrier side from the start, dominating possession and forcing Bayern to yet another error-ridden display in midfield.
The visitors had a good chance in the fifth minute when Kuranyi fought off defender Martin Demichelis and tried to curl a shot past keeper Hans-Joerg Butt who got a touch to it and sent it wide.
Bayern lacked spark yet again, though managed to score with their first real offensive effort in the 31st minute.
Badstuber's deep cross landed on Kuranyi's head before falling nicely for Van Buyten to fire in from close range.
TEENAGER SCORES
Magath, a former Bayern coach sacked in 2007 after winning back-to-back championship and Cup doubles, remained calm as his team regained their composure and levelled through Matip, the third player to be plucked from Schalke's youth teams this season.
Matip joins Schmitz and Christoph Moritz as players to have successfully made the transition this season.
Substitutes Arjen Robben and Mario Gomez added pace to Bayern's game but the hosts lacked patience as they desperately poured forward in the final 20 minutes in search of a winner.
"Our aim was to beat Schalke and we did not do it," said Bayern coach Louis van Gaal. "It is frustrating again that we did not score in the second half. We deserved a goal then."
Champions VfL Wolfsburg battled from a goal down to beat hosts Hoffenheim 2-1 thanks to a goal from Brazilian Grafite, who ended his goal drought stretching back to September 12.
Zvjezdan Misimovic had levelled five minutes earlier after Vedad Ibisevic had given Hoffenheim a first-half lead. Wolfsburg moved up to fifth on 21 points.
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