The Brazilian powered home from around 45 yards as the home side turned around a 1-0 deficit to take all three points. Ivica Olic had levelled for Dieter Hecking's side after they had gone behind to Stefan Aigner's goal.
The visitors looked buoyed by recent results, which have come off-the-back of their European exit to FC Porto.
They had the ball in the Wolfsburg net after eight minutes when Martin Lanig headed powerfully into the net - but was flagged for offside.
Just before the clock struck 15 minutes, Frankfurt were officially ahead as right-sided midfielder Aigner finished past Max Grun, who was standing in for Diego Benaglio.
Before the half hour mark, Wolfsburg missed a golden chance from 10 yards when Ivan Perisic beat the offside trap and charged away from his markers, before laying the ball off to Maxi Arnold - who could not steer the ball on target.
The second half belonged to Wolfsburg, who looked fired up after the break.
Croatian striker Olic scored another valuable goal on 69 minutes to level the scores after a fantastic pass from Belgian ace Kevin de Bruyne.
With chances few and far between, set-pieces were a possible route to goal and Naldo shot over the crossbar with 11 minutes remaining.
However, he would find the target in stoppage time as he brought the ball out of defence and went for a spectacular strike which sailed into the top corner of the goal.
As a result, Wolfsburg move one point behind Bayer Leverkusen - who drew with Eintracht Braunschweig - in the race for fourth spot.