The Wolves came from a goal down to win 2-1 on Sunday, denting Schalke's impressive start to the season and preventing them joining Bayern Munich and Werder Bremen at the top of the table.
Raul put the visitors ahead in the 13th minute, but two goals from Mario Mandzukic turned the game on its head.
The win was particularly satisfying for Magath, who left the Royal Blues under a cloud in March.
"At the beginning Schalke were the better team," Magath told Wolfsburg's official website.
"It was clear to see that the opponents' self-confidence was high having gone into the game on the back of three wins.
"Eventually, though, we worked our way back into the game and we gave more than our opponents. The win may have been slightly fortunate in the end but by no means undeserved."
Schalke coach Ralf Rangnick felt his side only had themselves to blame for the defeat.
"We clearly controlled the game in the first half and deservedly took the lead, but we then failed to make use of the situation," he said.
"Instead of continuing to play direct attacking football going forward, we played far too many unnecessary back passes.
"It was at that phase of the game that we missed out on the chance to seal the deal. After the equaliser there were chances at both ends but we still didn't play clearly enough and maybe just didn't put enough in."