Julian Draxler, fresh off the substitutes' bench, scored with a close-range effort to help give Dieter Hecking's men maximum points from a match they probably should have lost in truth, at the Volkswagen Arena.
In a cagey affair packed with half-chances for both sides, it should have been Bayer Leverkusen in-front, but they struggled to convert their chances and fell behind shortly after the half-hour mark, courtesy of an extraordinary moment of controversy.
Wolves steal undeserved and controversial lead
Nicklas Bendtner slammed home from a few yards out, but his reaction after hitting the back of the net spoke volumes about the goal itself. Not only was it against the run of play, but Vieirinha, credited with the assist, was in an offside position when the ball was played into his path.
The officials waved play on despite replays showing André Schurrle passed the ball into his feet - as opposed to the Leverkusen defender - and after he drilled the ball low into the former Arsenal man's path, he simply couldn't miss.
Chicharito draws visitors level before interval
The visitors got their deserved goal soon afterwards, with Mexican forward Javier Hernandez peeling away from Naldo within a flash in the area before expertly heading his effort past Diego Benaglio to level proceedings from a teasing ball by Christoph Kramer. His sixth goal in four matches, Chicharito has certainly been in amongst the goals recently since his summer switch from Louis van Gaal's Manchester United.
The final few minutes of the first-half were action-packed and end-to-end, and Benaglio made a great stop to deny Admir Mehmedi's one-on-one opportunity with just seconds until the interval.
As the second 45 began, neither side made any alterations. Papadopoulous made an important block to deny VfL Wolfsburg from taking the lead once more, and you could tell what it meant to the young Greek defender - as he celebrated passionately to the supporters behind the goal.
Schurrle squandered a golden opportunity to put the game to bed, curling his effort narrowly over the crossbar, whilst the hosts had two penalty decisions correctly turned down by the referee Manuel Graefe, who had a tough test having to keep up with the action at times.
Draxler on hand to seal maximum points
With little over fifteen minutes to play, and the scores still somehow level, Hecking made a double alteration. Draxler and Dutch forward Bas Dost were introduced into the fray, in place of Maximilian Arnold and the ineffective Nicklas Bendtner - who, apart from his goal, was quite frustrating in-front of goal and should have done more, in truth.
Just minutes afterwards, Wolfsburg celebrated as Draxler made it two-one, and Leverkusen were staring defeat in the face again. Wendell, Karim Bellarabi and Kevin Kampl tried their luck - to no avail, as Benaglio was alert to their efforts and ensured he didn't concede more.
The goal itself, is certainly going to be one that Bernd Leno will not want to see again. Ricardo Rodriguez took a pop from range, and although it bounced in-front of him, the goalkeeper parried it into a dangerous position yards away from his near post. Dost was on hand to flick the ball back goalwards, and Draxler was first to the ball, tapping home from close-range.
Should Wolfsburg had won? Probably not. Did they? Yes. Fine margins in football, triumph once more.
Both sides have respective Champions League fixtures in midweek - Wolfsburg travel to the Netherlands for a tough test against PSV Eindhoven; who they beat in matchday three of the group stages. Roma entertain Leverkusen on Wednesday meanwhile, with Roger Schmidt's side sitting second in their group, behind the competition's holders Barcelona.