The Royal Blues, who last week earned their first point of the season, looked sharper in the first half than in past weeks and went ahead with 19-year-old Malick Thiaw's diving header at the far post in the 30th minute.
A handball by Salif Sane gave the visitors a penalty in the 56th and Nicolas Gonzalez stepped up to equalise.
Stuttgart then took complete control of the game, with Schalke pulling back deep into their own half, and would have left with all three points were it not for Schalke goalkeeper Frederik Ronnow's fine saves late in the game.
Stuttgart move up to fourth place on nine points while Schalke are 17th with two after six games.
Leaders RB Leipzig, on 13 points, travel to Borussia Moenchengladbach on Saturday when champions Bayern Munich, a point behind, visit struggling Cologne.