Dieter Hecking's side moved into fifth, good enough for a UEFA Europa League spot, as the away side made it seven league matches unbeaten.
Freiburg went into the encounter having won only twice in 14 top-flight matches this season and never looked likely to improve that record.
The visitors took only eight minutes to break the deadlock as Maximilian Arnold diverted Patrick Ochs' low right-wing cross past the helpless Oliver Baumann in goal.
Their second arrived just three minutes later when Luiz Gustavo broke into the area and squared to Ivica Olic, with the experienced Croatian alert to prod into the net.
Wolfsburg were made to wait for their third goal, but it did eventually come in second-half stoppage time when, after good work by Willi Evseev lured Baumann out of his goal, Marcel Schafer knocked into an empty goal.
In Sunday's only other match, Hertha Berlin picked up a 2-0 win at 10-man Eintracht Braunschweig to jump up to seventh place, while their hosts stay bottom of the league.
Hertha made the breakthrough after 20 minutes when Ronny's out-swinging free-kick dropped invitingly just past the front post and Adrian Ramos stooped down to direct a header beyond Daniel Davari for his eighth league goal of the campaign.
The visitors made sure of the win in the 80th minute and Ronny was instrumental again as he raced towards Eintracht's penalty area on the counterattack before playing Tolga Cigerci into the danger area, who duly slotted home.
Timo Perthel picked up a second booking shortly after to rub salt in the wound.
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