The Belgian moved to 20 league assists for the season after setting up Daniel Caligiuri and Naldo for the decisive goals either side of Pierre-Emerick Aubameyang's penalty
Goals early in each half from Daniel Caligiuri and Naldo proved enough for the home side to triumph at the Volkswagen Arena in a dress rehearsal for the DFB-Pokal final.
Pierre-Emerick Aubameyang fired home a penalty to level the scores in the first half after Diego Benaglio had taken down Kevin Kampl in the box, with the Wolfsburg goalkeeper perhaps fortunate not to see red for the offence.
The visitors huffed and puffed in a bid to find a second equaliser, with manager Jurgen Klopp throwing on the fit-again Marco Reus with 20 minutes to play.
However, they were unable to get back on level terms again, and the defeat leaves them three points behind sixth-placed Augsburg in the Bundesliga table with just one round of fixtures to go.
Wolfsburg will end the season unbeaten at home in the league, having made a swift start to proceedings and broke the deadlock inside the first minute.
Kevin de Bruyne was given enough time and space on the left wing to send in a low cross towards the supporting Caligiuri, who had the simple task of steering the ball past Mitchell Langerak in the visiting goal.
But, while the pre-Christmas Dortmund may have folded after conceding so early, Klopp's in-form side instead responded impressively.
They did not have long to wait to get back on level terms as Kampl burst behind Wolfsburg's back four and beat the onrushing Benaglio to the ball, the goalkeeper's clumsy contact giving referee Marco Fritz little option than to point to the spot.
Aubameyang tucked away the resulting spot-kick, sending Benaglio the wrong way.
The score remained 1-1 through to the break, though Aubameyang wasted a glorious chance to double both his and Dortmund's tally, somehow heading Henrikh Mkhitaryan's right-wing cross wide with the goal at his mercy.
It did not take long after the interval for the home team to punish Aubameyang's miss and move in front again.
Naldo got Wolfsburg's second goal, the defender – who also netted in the 2-2 league draw between the sides earlier in the season - turning to fire in a loose ball with his left foot after Dortmund had failed to deal with a corner.
De Bruyne made Bundesliga history in the process, matching the record of 20 assists in a single league campaign. He missed out on his 21st despite taking the decisive corner.
The closest Dortmund came to making it 2-2 was from a set-piece of their own, Sokratis Papastatolpoulos scuffing wide after a free kick had dropped nicely into his path.
Dortmund host Werder Bremen next week. A point will be enough to secure Europa League football as Klopp warms up for May 30's Pokal final, where revenge for this defeat will be just one thing on his mind as he leads the club for the final time.