Leverkusen started brightly but fell behind after just eight minutes when defender Nordi Mukiele headed Mohammed Amoura's dangerous header into the wrong net.
The Werkself responded well and equalized six minutes later after Wolfsburg failed to clear the ball out of their area, allowing Granit Xhaka to find Florian Wirtz, who curled the ball into the bottom left-hand corner from the edge of the box, reports Xinhua.
The Wolves continued to wait for a counterattack as the defending champions began to gain the upper hand as the game progressed.
Both goalkeepers had their hands full of work as Kamil Grabara denied Patrick Schick and Wirtz in quick succession on the half-hour mark, before Amoura shot wide from a promising position.
The hosts completed their comeback moments later when Jonathan Tah headed home Alejandro Grimaldo's corner to make it 2-1.
Leverkusen's lead didn't last long, however, as Sebastiaan Bornauw's header leveled the scores in the 37th minute, before Matthias Svanberg's 18-meter strike gave the Wolves a 3-2 lead on the stroke of halftime.
After the restart, Leverkusen coach Xabi Alonso reacted by bringing on Piero Hincapie, who made an immediate impact to level the scores at 3-3 four minutes into the second half.
Yannick Gerhardt was shown a straight red in the 88th minute for a rude challenge on Jeremie Frimpong, before Xhaka's long-range shot hit the left post three minutes later.
Leverkusen had the last laugh when a deflected ball landed in front of Viktor Boniface, who turned on his axis with superb technique to slot home the 4-3 winner in stoppage time.
"On the one hand, I'm satisfied and happy with three points. On the other hand, I'm not happy with our performance, especially in the first half. The second half was better. Overall, it wasn't our best performance," said Alonso.
Elsewhere, on Sunday, Stuttgart stunned Borussia Dortmund 5-1 thanks to Deniz Undav's brace, while newly promoted St. Pauli shared the spoils after a goalless draw with Leipzig.