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The same duo combined with 10 minutes of the first half to go as Trochowski lofted a ball in towards Bacca, who was denied a simple tap-in by some fine defending from Matthias Ginter.
Trochowski was himself denied just before the break, with Baumann making another good stop to ensure that the sides went into the halfway stage all square.
There was nothing that the Freiburg keeper could do about the opening goal, however, as Fallou Diagne pulled Bacca to the floor inside the box, receiving a second yellow card to earn his marching orders as well as conceding a penalty.
Diego Perotti stepped up to the spot kick and made no mistake from 12 yards to give his side a 1-0 lead.
Marko Marin had a fine chance to wrap the game up for the hosts when he was sent through on goal in the 87th minute, but his delicate chip went onto the bar when he should have scored.
Bacca was guilty of making the same mistake moments later when he also went for a chipped finish, but he too saw his effort come back off the crossbar.
The Colombian made up for the miss in the first minute of stoppage time, however, completing the scoring by rolling the ball into an empty net following good work by Jairo Samperio.