Leon Goretzka put the Royal Blues ahead against the run of play in the 28th minute before an own goal from Felipe Santana gave Leverkusen a deserved equaliser.
Klaas-Jan Huntelaar scored once again while Leverkusen were dominating, earning Schalke their fourth consecutive win in 2014 and inflicting Leverkusen's second defeat of the new year.
Leverkusen started well, but a mistake by Lars Bender undid all their good work.
He gifted the ball to Goretzka, who skipped past the lunge of Philipp Wollscheid on his way towards Bernd Leno, finishing off the move with a delightful chip over the Leverkusen goalkeeper.
It was a cruel blow to Leverkusen, who had gone close to opening the scoring through a Sebastian Boenisch header only moments earlier.
The home side made their intentions clear at the start of the second half with a string of openings, the best of which was wasted by Stefan Kiessling, who turned inside keeper Ralf Fahrmann but was unable to stay on his feet to turn the ball into the unguarded goal.
Leverkusen kept the pressure on and Santana made a fine goalline clearance to keep Boenisch's header out, earning applause from the Schalke players warming up behind the goal.
He was not their hero seconds later, though, when he turned the resulting corner into his own goal with his thigh.
It was a deserved equaliser for Leverkusen, who pushed for a second and Gonzalo Castro should have got it when he was put through on goal, but sliced his shot wide with only Fahrmann to beat.
Despite spending the second half penned in their own half, as soon as Schalke got the chance to break out with a free-kick, they took the lead again in the 74th minute.
Jefferson Farfan curled a free-kick into the box and Huntelaar, with his back to goal, expertly guided it beyond Leno with his head.
Leverkusen continued to dictate proceedings and, on the cusp of the 90th minute, Simon Rolfes saw his shot deflected over before Omer Toprak headed against the crossbar.
For all their efforts, Leverkusen were unable to find an equaliser, leaving them wondering how they had not managed even to get a point.