Xabi Alonso’s side ended a run of three Bundesliga games without a win following the hard-earned victory.
Boniface salvaged himself by hitting target 18 minutes from time after missing from the spot on nine minutes.
The 23-year-old has now scored five goals in seven league appearances for Die Werkself this season.
The forward was replaced by Patrick Schick 10 minutes from time.
His compatriot, Nathan Tella took the place of Jeremie Frimpong in the 80th minute.