Bendtner - who has struggled to establish himself with the DFB-Pokal holders - made his case for a starting berth with a well-taken equaliser followed by the crucial spot-kick amid a dramatic finale as Wolfsburg were 5-4 victors in the shootout.
Arjen Robben - featuring for the German champions for the first time since April after a muscular injury - had given Bayern the lead early in the second half following an action-packed opening period in which both sides spurned opportunities.
For much of the second it seemed a lack of cutting edge would haunt Wolfsburg - who named Kevin De Bruyne in their XI following injury concerns.
However, substitute Bendtner was on hand to convert the Belgian's pinpoint cross following a sweeping counter-attack down the right to take Bayern to penalties.
Debutant Arturo Vidal got Bayern off to a good start in the shootout, but team-mate Xabi Alonso was the only one not to score - Wolfsburg's reserve goalkeeper Koen Casteels saving well with his foot in Diego Benaglio's injury-enforced absence.
It allowed Bendtner to convert the winning penalty and give Dieter Hecking's men a confidence boost as they seek to run Bayern closer in the Bundesliga this term.
Bayern handed a competitive debut to Douglas Costa and the Brazilian showed electric pace early on to set up a sight on goal for Alonso.
The Spaniard sent a scruffy shot wide, but Bayern continued to threaten, Jerome Boateng rattling the crossbar after Thiago Alcantara's header fell to him inside the penalty area.
Vieirinha - given a torrid time by Costa early on - asked questions of his own at the other end when he blasted Wolfsburg's first effort narrowly off target from distance.
Costa wasted a great opportunity when he passed to Robert Lewandowski instead of shooting when through on goal and, as the chances flowed, Manuel Neuer was required to keep out a wicked deflection off Medhi Benatia.
The final chance of a gripping half fell to De Bruyne - the in-demand Belgian shooting wide with an open goal at his mercy after Neuer and Benatia made a mess of clearing a bouncing ball.
Somehow, the sides were level at the break, but Bayern needed just four minutes of the second half to take the lead, Robben snaffling up his chance after Lewandowski's close-range effort was spilled by Casteels.
The energetic Costa was again pivotal down the left and, while Wolfsburg continued to threaten, Bas Dost latched onto De Bruyne's incisive pass only to shoot straight at Neuer.
Eventually, Wolfsburg were rewarded one minute from time when Bendtner converted De Bruyne's cross and his evening got better when he sealed the win.
Alonso's saved penalty proved costly as Bendtner followed Ricardo Rodriguez, De Bruyne, Andre Schurrle and Max Kruse in beating Neuer to ensure Wolfsburg's first Supercup success.
