Dortmund made two changes from their loss against Union Berlin, as striker Erling Haaland returned from his injury alongside a recall for Thomas Delaney.
Marco Reus had an early chance to grab the lead for the hosts in the tenth minute after receiving a pass inside the box but his thumping effort was brilliantly saved by shot-stopper Koen Casteels.
Wolfsburg had a penalty appeal midway through the first stanza that was referred to the Video Assistant Referee (VAR) after a ball hit the hand of Axel Witsel inside the box but a penalty was not given after review.
Edin Terzic's charges were creating big chances towards the end of the first stanza but they were repelled by Casteels and Jadon Sancho who should have given the hosts the lead in first-half stoppage time but somehow missed the target with a close range opportunity.
BVB continued to put Wolfsburg under pressure coming from the break and Haaland came close to breaking the deadlock eight minutes from the break with a strike towards the top corner after a through ball inside the box but his effort was kept out by Casteels.
Manuel Akanji finally got the breakthrough for Dortmund in the 66th minute with a stunning header at the near post from a corner by Sancho.
Wolfsburg were getting out of their defensive shell after going a goal down and Paulo Otavio nearly snatched the equaliser in the last 18 minutes with a strike from outside the box that was saved by shot-stopper Roman Burki.
The visitors were vulnerable to counter-attacks in the latter stages and they were punished in the last minute after Sancho went through on goal and drilled his strike into the bottom corner to seal all the three points for Dortmund, who went up to fourth on the log.