Sven Bender had given Jurgen Klopp's men an early lead but the Wolves responded in remarkable fashion as Ivan Perisic scored twice against his former club before Naldo smashed in a third before half-time.
The visitors had been made to pay for some sloppy defending but Marco Reus refused to give up and brought his side back from the dead with two late goals earning a point to ensure his side finish the season as runners-up.
Wolfsburg started brightly and were perhaps unfortunate to fall behind to BVB's first attack with just five minute played. Reus' short free kick was swung into the box by Nuri Sahin and Bender eluded his marker at the back post to poke the ball across goal and inside the far corner.
The hosts remained positive, though, and were not behind for long as a tidy move saw them restore parity nine minutes later. Makoto Hasebe released Ivica Olic inside the area who then showed great intelligence to roll the ball to the back post with his first touch, enabling Perisic to add a simple finish.
Robert Lewandowski hesitated when presented with a chance to regain Dortmund's advantage soon after and it proved extremely costly as Dieter Hecking's side struck twice in quick succession.
With 22 minutes on the clock Perisic was afforded too much time 25 yards from goal and his effort took a wicked deflection off Diego, wrong-footing the idle Roman Weidenfeller and dropping into the net.
It only took another four minutes for Wolfsburg to send the home fans into raptures with a third. Felipe Santana failed to stay close to Naldo from a corner, leaving the towering center back with space to bring down Jan Polak's flick on and rifle the ball past the keeper.
The BVB defense was having a torrid afternoon and Santana came desperately close to making it even worse when his header came back off the frame of his own goal.
Minutes before the break the Brazilian would have breathed a sigh of relief as, after failing to pick up Olic's run, the striker sent the ball wide of the post after an exquisite pass from Ricardo Rodriguez.
Klopp introduced Jakub Blaszczykowski and Julian Schieber for the second half and BVB instantly looked more threatening. However, Diego Benaglio produced a fine stop to keep out Lewandowski three minutes after the break.
Despite Dortmund's fluency beginning to grow, the Wolves proved dangerous on the break and so there was a sense that the next goal would be key. Polak and Schieber both had opportunities to swing momentum the way of their respective sides before the hour mark, but neither could hit the target.
The visitors' energy levels soon decreased as a compact, stout Wolfsburg defense repelled the ball time and again.
But Dortmund conjured up the same spirit which saw them past Malaga en route to the Champions League final, with Reus spearheading a dramatic comeback.
After latching onto a brilliant pass from Gundogan and looping an effort over an indecisive Benaglio in the 84th minute, Reus grabbed a second with two minutes of normal time remaining as he danced into the area and slammed an effort in off the crossbar.
The point ensures that BVB finishes the season in second position, despite falling 22 points behind Bayern Munich.