It was the visitors that took an early lead when Marcel Heller rounded off a fantastic move to put his side in front. Saed Kolasinac got the equaliser for the Royal Blues before the half hour mark.
In the second half, goals from Maxim Choupo-Moting and Alessandro Schopf rounded off a perfect afternoon for the home side - who are now 12 games unbeaten across all competitions.
Visitors stun the hosts
The start of the game didn't go to plan for the hosts as the visitors took a surprise lead with only six minutes on the clock.
The goal came from a counter-attack as the visitors broke quickly from defending a corner and a bit of quality from Sandro Sirigu played Heller in on goal and he made no mistake as he rounded the goalkeeper and put the ball into the net.
Kolasinac got the hosts back on level terms
It took a while for the hosts to show some kind of response but they got back on level terms before the half hour mark.
Left back Kolasinac scored his first goal of the season as he headed home a brilliant cross from Choupo-Moting to level things up.
From there, the real Schalke turned up and they were unlucky to not be in front when a brilliant header from Leon Goretzka was saved on his own bar by goalkeeper Michael Esser.
In the same move though the hosts were awarded a penalty when Goretzka was brought down in the box after the ball was whipped back into the box.
Choupo-Moting stepped up to take the penalty but he missed as Esser read his intentions and saved with his legs to keep his side on level terms.
The remainder of the half saw a lot of frustration from the home crowd as the hosts really struggled to get the second goal before half-time and went in level.
Choupo-Moting and Schopf seal another victory for the hosts
The struggle continued at the start of the second half for the hosts as they struggled to create anything until Markus Weinzierl made a tactical change to his side by going with three at the back.
This worked almost immediately as Choupo-Moting made up for his first-half penalty miss by putting his team in front. The goal was created by the impressive Max Meyer who drove into the box and played a nice cross into the striker who made no mistake this time around.
After the second goal, both teams lacked to quality to get any more goals until a moment of magic right at the end of the game saw Schalke seal the three points.
Yevhen Konoplyanka played a wonderful through ball to Schöpf, who made no mistake by sticking the ball into the net past the helpless Esser.
That was literally the last kick of the game as once again the Royal Blues passed yet another test to come behind and continue their good run going in recent weeks.