Two goals in five second-half minutes to secure all three points for Uwe Rosler's team.
The visitor is now without a win in nine Bundesliga games, but had the better of the early exchanges with the pace of welsh youngster Rabbi Matondo causing Dusseldorf plenty of problems. The first half ended 0-0.
American defender Weston McKennie created the first chance of note for Schalke at the start of the first half. However, his drilled shot flew wide. It wouldn't be long until McKennie had another chance, firing Schalke into the lead. After peeling away at the back post, the United States international pulled off a diving header to give David Wagner's team the advantage.
Fortuna ramped up the pressure and ten minutes later found parity as Rouwen Hennings scored his first goal of 2020. A fierce 40 yard free-kick from Kevin Stöger was parried by keeper Markus Schubert, with Hennings on hand to nod in from close range.
Schalke switched off as it conceded minutes later, as Kenan Karaman headed in a winner for the struggler with 68 minutes on the clock.