Croat Kramaric, making his comeback from injury, fired in on the rebound in the 72nd minute and against the run of play after Schalke keeper Alexander Nuebel had palmed Bebou's shot into his path.
The Togolese then drilled in their second goal in the 86th after a defensive blunder and a fine solo run.
Schalke's Daniel Caligiuri hit the woodwork with a free kick and Alessandro Schoepf headed narrowly over the bar as Schalke dominated the first half and had a string of scoring chances.
But Hoffenheim scored with their first real chance through Kramaric. Bebou completed their second consecutive big win, after also stunning Bayern Munich in the previous matchday.
In a tight title race Borussia Moenchengladbach remain top on 16 points, along with VfL Wolfsburg.
Champions Bayern, who drew 2-2 at Augsburg on Saturday, are in third on 15, as are Dortmund and RB Leipzig. Schalke are a point behind while Hoffenheim move up to 11th on 11.