The result kept Dortmund a point short of securing second spot with two games remaining, with the Ruhr valley club in second place on 63. It also handed Bochum their first win at Dortmund since 1998.
In a seven-goal, drama-filled encounter Erling Haaland scored a hat-trick to carry Dortmund from 2-0 down to lead 3-2.
The hosts quickly recovered and pulled a goal back with Haaland's 16th-minute penalty.
The Norwegian was far from done and he bagged his second with another spot kick on the half-hour mark.
The 21-year-old thought he had completed their comeback with a tap-in and a lucky bounce in the 62nd but Bochum came back once more, levelling though Juergen Locadia in the 81st and Pantovic's penalty for a memorable win in the local derby.