Boniface thought he had opened the scoring before half-time, only for VAR to disallow the goal.
However, the forward made no mistake in the 51st minute, finishing off a well-placed cross from Jeremie Frimpong to give the German champions the decisive lead.
Elsewhere, Milan’s rivals Inter Milan secured a resounding 4-0 victory over Crvena Zvezda at the San Siro, with Hakan Çalhanoğlu, Marko Arnautovic, and Lautaro Martinez all on the scoresheet.
It marked Inter’s first win of the campaign, pushing them back into contention for the knockout stages.
Barcelona, still smarting from an opening-night loss to Monaco, bounced back emphatically with a 5-0 demolition of Young Boys.
Robert Lewandowski was clinical, scoring twice early in each half to spearhead the dominant display. The win puts Barcelona back on track.
Meanwhile, PSV Eindhoven picked up their first point of the season, drawing 1-1 with Sporting Lisbon. Dutch midfielder Jerdy Schouten gave PSV the lead before the Portuguese side equalised late.
French debutants Stade Brest continued their stunning run in the competition, cruising to a 4-0 victory away to Salzburg.
Abdallah Sima stole the show, netting twice to keep the French side’s perfect record intact.
In another fixture, VFB Stuttgart were held to a 1-1 draw by Sparta Prague.
