The visitors looked dangerous in the early stages, and their pressure was rewarded in the eighth minute when Kevin De Bruyne spotted the run of Daniel Caligiuri, who remained calm in front of goal to slot home.
Despite almost losing their advantage, Wolfsburg remained on top, and were inches away from doubling their lead just before the break when De Bruyne rattled the woodwork with a free kick.
The hosts enjoyed an extended spell of control early in the second half, but they missed a golden chance to equalise when Mike Frantz struck his effort straight at Benaglio after beating the offside trap.
Caligiuri punished Freiburg for failing to turn their pressure into a leveller as he helped himself to a second goal with an emphatic finish from just inside the box midway through the second half.
Sebastian Kerk set up a dramatic finish by curling a free kick into the top corner in the first minute of stoppage time, but Wolfsburg held on to secure a deserved win.