Fellow new signing Sebastian Rode was also on target as Pep Guardiola's side marched to a comfortable triumph against their Bundesliga rivals
Lewandowski, who has made an impressive start since arriving from Borussia Dortmund earlier this month, scored twice, while Rode opened his account in a comfortable victory at Hamburg's Imtech Arena.
Bayern shot out of the blocks and were ahead four minutes in when Lewandowski scored his third goal in as many games for the German champions.
Rode duly got in on the act and scored his first goal since joining from Eintracht Frankfurt, while Lewandowski added a second before the break to effectively secure the pre-season trophy for Pep Guardiola's men.
Lewandowski's first goal, in a game played over 60 minutes rather than the usual 90, came courtesy of a header from Franck Ribery's fine cross.
And the defending champions doubled their advantage when Rode produced an expertly curled finish past Max Grun in the Wolfsburg goal - Claudio Pizarro having intricately backheeled the ball into his path.
Guardiola saw his side continue to dominate as they moved 3-0 ahead within 20 minutes - Lewandowski again on target.
Afforded far too much time, the Poland forward curled home a strike from outside the area to all but wrap up the win.
Wolfsburg rallied late in the half and enjoyed their strongest spell of possession, but struggled to get in behind the Bayern defence with any regularity.
Despite failing to reel Bayern in during the second half, Wolfsburg were at least able to prevent their opponents from pulling further clear.
Guardiola will no doubt take heart from seeing Ribery manage 54 minutes on his second game back from injury, while Lewandowski's scoring streak provides a further boost with the German Super Cup against Dortmund approaching on August 13.