Bayer Leverkusen's Nigerian forward #22 Victor Boniface (C) celebrates scoring the 4-3 during the German first division Bundesliga football match between Bayer Leverkusen and VfL Wolfsburg in Leverkusen. AFP
In a seesaw encounter, the teams were locked at 3-3 from the 48th minute.
Wolfsburg were then reduced to 10 men in the dying stages when Yannick Gerhardt sunk his studs into Jeremie Frimpong's calf.
Boniface, who came on with 22 minutes remaining, collected a pass before pivoting on the spot and shooting home to snatch the German champions another late victory.
Leverkusen midfielder Granit Xhaka was far from pleased with the win, calling the result "a giant wake-up call -- none of us can be satisfied with the game today.
"We can't keep going with performances like that. We can't defend so naively. Sure, we scored four but we can't do that every weekend."
Leverkusen coach Xabi Alonso had named a heavily changed line-up from the side which thrashed Feyenoord 4-0 in the Champions League on Thursday, giving Nordi Mukiele his starting debut.
However, Mukiele, signed on loan from French champions PSG, endured a nightmare start when he allowed the ball to bounce in off his thigh for a fifth-minute own goal.
Florian Wirtz, who scored a brace on his Champions League debut on Thursday, drew Leverkusen level with a superb effort from outside the box shortly after.
Jonathan Tah headed the hosts ahead from a corner after 32 minutes but Leverkusen's joy was short-lived, with Wolfsburg's Sebastiaan Bornauw equalising five minutes later, jumping above Mukiele to head in from close range.
Mattias Svanberg scored from the edge of the box on the counter for Wolfsburg before Leverkusen levelled again on 48 minutes through Piero Hincapie.
In breaking through for their debut Bundesliga title last season without losing a match Leverkusen dropped just 12 points but they appeared on course for a second setback after losing to RB Leipzig in their last home game.
Boniface had other ideas and sliced the ball home in the third minute of injury time to keep Leverkusen three points behind league leaders Bayern, ahead of next week's clash in Munich.
Later on Sunday, Borussia Dortmund travel to Stuttgart while St Pauli host RB Leipzig.
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