Dortmund took an early lead and looked like certain winners when they went 2-0 in front and displayed pure dominance in second half, however, another moment of brilliance by Dejagah brought Wolfsburg back into the match.
The Iranian international received the ball on the right wing and sent one of his trademark crosses to the center, where Mandzukic scored from close range.
Wolfsburg now put pressure on the guests and seemed to be close to an equalizer, especially when Dejagah showed great footwork on the flank to get past his marker and crossed the ball to the unmarked Mandzukic near the penalty spot, but the Croatian international somehow hit over the ball.
The homeside was reduced to ten men after Madlung's second yellow card late in the game, however, didn't give up until conceding the decisive third goal following a double-blunder from left midfielder Schäfer.
The loss was a setback in Wolfsburg's fight for a UEFA Europa League spot next season, as they are three points behind a qualification spot again.
However, Dejagah wasn't only once more the best Wolfsburg player on the field, he also moved to third position of Bundesliga's assist ranking with ten assists. Only Franck Ribery (17 assists) and Thomas Müller (12) of Bayern Munich have more assists to their name this season.
In Spanish La Liga, a horrible Osasuna side suffered a 0-6 thrashing in the hands of Rayo Vallecano.
Nekounam, who like the complete team, had an off-day and was subbed out at halftime, when Osasuna were already trailing by four goals.