The Dutchman, who had not scored in 1,199 minutes and since November last year, put them ahead in the ninth minute and came to the rescue again in the 78th after Stuttgart had struck twice.
Stuttgart's Florian Klein then gifted them the three points in the 89th minute, turning a Kevin-Prince Boateng shot into his own net.
The result keeps Schalke in fifth spot on 45, two ahead of sixth-placed Augsburg who drew 0-0 against Cologne. Stuttgart are last on 27.
Hoffenheim and Borussia Dortmund shared the spoils after their 1-1 draw to stay on 41 and 40 points respectively in the hunt for a top six finish that leads to Europe with three games left in the season.
Werder Bremen leapt to seventh on 42, spoiling former long-time coach Thomas Schaaf's return to the Weser stadium, with a 1-0 victory over Eintracht Frankfurt courtesy of Davie Selke's 66th minute goal off his chest.
A possible seventh place could be up for grabs if VfL Wolfsburg win the German Cup.
The Wolves, in second place, squandered a two-goal lead in their 2-2 draw against Hanover 96, who scored a stunning equaliser through Salif Sane's bicycle kick, but are all but guaranteed a Champions League group spot.
The are on 62 points, five ahead of Borussia Moenchengladbach in third, who are in action at Hertha Berlin on Sunday.
Champions Bayern Munich travel to Champions League hopefuls Bayer Leverkusen later on Saturday.
(Reporting by Karolos Grohmann, editing by Alan Baldwin)
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