Leverkusen's 38-game unbeaten streak seemed in jeopardy when they trailed 1-0 with less than five minutes of regular time left.
Robert Andrich equalized for the league leaders in the 88th minute, cancelling out Maximilian Beier's opener.
The hosts completed their comeback with a 91st-minute winner from Patrik Schick.
They sit 13 points ahead of Bayern Munich, who are set to face Borussia Dortmund later on Saturday.
Leverkusen played their first match since manager Xabi Alonso confirmed he would stay at the club next season, ending speculation about a move to Liverpool or Bayern Munich.
Seventh-placed Hoffenheim dampened the mood surrounding Alonso's decision when Beier connected with Wout Weghorst in the penalty area before finding the net past goalkeeper Lukas Hradecky.
Leverkusen piled on the pressure, and quick-fire goals from Andrich and Schick ensured the club extended their unbeaten run to 39 games across all competitions.
With just seven games remaining this season, Leverkusen are on track to secure their first league title.
