The Bundesliga champions, who entered the match against last season's second placed team carrying a 100 per cent record, were disappointing as they fell behind to a goal from Daniel Caligiuri in the first half - prompting coach Pep Guardiola to make a pair of changes during the interval.
The Bayern coach replaced midfielder Thiago Alcántara with the Poland international in search of more potency from his side but could not have forseen what would happen next.
The 27 year old needed only six minutes to draw Bayern level after reacting to a loose ball from former team-mate Dante to slot home - before firing his team into the lead with a drilled shot from outside the area only a minute later.
Lewandowski completed his hat-trick in just four minutes - the fastest ever scored in Bundesliga history - although he needed three attempts having been denied by the post and then a save from Wolfsburg keeper Diego Benalgio before finding the net.
The previous fastest hat-trick was scored by Duisburg's Michael Toennies in 1991 during a six-minute spell. Toennies, through his former club, was quick to congratulate the new record holder, telling Lewandowski: 'You deserved it.'
The Pole's haul was also four times faster than the Premier League record for five goals in a game, set by Jermain Defoe in 2009. Defoe hit five in 36 second-half minutes for Tottenham during a 9-1 win over Wigan.
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