Mathis Bolly gave the visitors a surprise lead late in the first half, but Wolfsburg's top scorer Ivica Olic earned his side a point in the 51st minute.
After a 5-2 win at Freiburg last weekend, the result will be regarded as a setback for Wolfsburg, who missed the chance to reduce the arrears on the top six to five points.
Fortuna will be pleased with a point which gives them an eight-point cushion over the bottom three.
Wolfsburg started brightly, but could not find a goal to crown their efforts.
The nearest they came was when Ricardo Rodriguez's shot hit a post with Fabian Giefer beaten.
Fortuna's defensive tactics did not appear to be getting them anywhere until Bolly gave them the lead against the run of play in the 37th minute, firing in after being set up by Robbie Kruse.
The fans inside the VW-Arena were stunned, but with six defeats and only two wins in 13 home games this season, they were getting used to seeing their side behind.
Their team, though, did not cave in, as has been the case on occasions this term, but instead searched for a route back into the game.
They found it in the 51st minute when Olic scored his fourth goal in his last three matches.
He then set up Bas Dost, who wasted a chance to give the Wolves an instant advantage, and that proved to be their last big chance of the game.
Dani Schahin missed a chance to steal all three points for the visitors when he tried to backheel the ball past Diego Benaglio in the last minute.