Promoted Leipzig looked well on the way to cutting the lead of Bayern, who drew 2-2 at home to Mainz 05 on Saturday, back to six points when Timo Werner put them ahead after 14 minutes.
Werner beat defender Benedikt Hoewedes to the ball to head in and cap a strong start with his 17th goal of the campaign.
The visitors did well to keep Schalke at bay in the first half but the hosts drew level a minute after the break with striker Klaas-Jan Huntelaar's second league goal this season.
Bayern are top with 70 points ahead of Leipzig on 62. Borussia Dortmund have jumped into third spot with 56 after Saturday's 3-2 win at Borussia Moenchengladbach.
The top three clubs win automatic qualification to the Champions League group stage, with the fourth-placed team going into the competition's qualifying rounds.
(Reporting by Karolos Grohmann; editing by Ken Ferris)
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