Schalke missed out on top place after being held to a 1-1 draw by Cologne in the previous round. This time, it failed to take advantage after Borussia Mönchengladbach, Wolfsburg, Bayern Munich, Leipzig and Freiburg all dropped points over the weekend.
Bebou, who came on for the second half, went past a host of challenges before testing Alexander Nübel in the Schalke goal in the 72nd minute. Andrej Kramaric rifled in the rebound from the goalkeeper's fine save.
A mistake from Benjamin Stambouli allowed Bebou to seal the result shortly before the end. The Togo forward ran onto the ball and eluded Salif Sané before firing inside the bottom corner. It was the second consecutive win for Hoffenheim, which stunned Bayern with a 2-1 win in Munich in the previous round.
Former United States international Wagner, who previously coached Huddersfield in England, was in charge of Hoffenheim Under-17s and Under-19s between 2007 and 2009. Earlier Sunday, Cologne beat fellow promoted side Paderborn 3-0 for its first victory at home.
Bayern was held 2-2 at Augsburg on Saturday, when Wolfsburg drew 1-1 with Leipzig to stay unbeaten and Borussia Dortmund held on for a 1-0 win over Gladbach. After eight rounds, Gladbach leads on goal difference from Wolfsburg with 16 points, followed by Bayern, Dortmund and Leipzig on 15 points. There are just two points between the top nine teams in the 18-club division.
More AP soccer: https://apnews.com/Soccer and https://twitter.com/AP_Sports
Ciarán Fahey on Twitter: https://twitter.com/cfaheyAP