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."
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.
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."
