Jefferson Farfan put the high-flying Royal Blues in front in the 33rd minute and goals from Ibrahim Afellay and Roman Neustadter in the second half earned them all three points.
Wolfsburg's fourth defeat of the season leaves them inside the bottom two after seven games while Schalke keep up the chase to the runaway league leaders Bayern Munich, edging three points clear of their local rivals Borussia Dortmund, their next opponents in a fortnight.
Magath left Schalke nine months after leading them to second in the Bundesliga and one of their best ever league finishes, but the side was no longer performing at those levels when he walked away.
One of those under-performers was Farfan, but he showed Magath what he is capable of with the opening goal in the 33rd minute.
The Peruvian headed in Christian Fuch's cross after being left completely unmarked at the far post, and made a point of expressing his joy to Magath on the Wolfsburg bench.
Ten minutes later, Lewis Holtby should have made it two when he broke away and took the ball past Diego Benaglio, but as he turned inside the last Wolfsburg defender, he lost his footing and the chance was gone.
Afellay opened his account for Schalke within 60 seconds of the restart after being put through on goal by Holtby, and the Dutch midfielder kept his composure to slot the ball low past Benaglio.
The third goal came in the 58th minute when Wolfsburg did not fully clear a corner and the ball came back to Neustadter, who at first struggled to get the ball out from between his legs, but when he did, he swept the ball in before his team mate Klaas-Jan Huntelaar did it for him.
Huntelaar hit the post and Benaglio denied Farfan as Schalke threatened to run away with it, and not even Srdjan Lakic could score a late consolation when he was left with only Lars Unnerstall to beat.