Oliver Barth opened the scoring for Freiburg after 30 minutes and it was 2-0 when Erik Jendrisek netted 10 minutes later. Cedrick Makiadi pushed the advantage to 3-0 after 59 minutes.
Freiburg dominated the proceedings from the start as Johannes Flum failed to strike into an empty net in the ninth minute and Cisse blasted his 13-yard shot off the right post 15 minutes later.
The hosts took the lead on the half-hour mark from a set-piece as Julian Schuster's free-kick went into the box where Barth headed in from nine yards.
Freiburg doubled the advantage five minutes before the break with Cisse streaking down the right side and crossing into the middle where Jendrisek had plenty of space to beat Wolfsburg keeper Diego Benaglio.
Cisse, who has stated his desire to leave before the transfer deadline, nearly made it 3-0 in first-half stoppage time but his volley went just wide.
Freiburg had one chance after another after the restart before Wolfsburg were close to pulling a goal back in the 56th minute but Patrick Ochs' shot hit the post.
Freiburg did pull ahead by three goals in the 59th minute as Christian Trasch tried to clear Maximilian Nicu's cross but the ball went right to Makiadi, who volleyed past Benaglio from 14 yards.
Cisse had another chance after 76 minutes but could not beat Benaglio with a header from five yards.