Lewandowski's Dortmund are at Bundesliga side Eintracht Frankfurt on Tuesday in the German Cup quarter-finals, but the Poland star's car problems came after he scored twice in Borussia's 5-1 league win at Werder Bremen last Saturday.
Reports in the German media say the 25-year-old had the wheels stolen from his Porsche Cayenne GTS, which is worth around €90,000 and was parked outside his Dortmund home, with only bricks left to keep the car off the ground.
Lewandowski's car was tipped forward during the suspected prank, badly damaging the front brakes.
The high jinx will not be cheap. A brand-new set of wheels will cost around €2,500 euros for Lewandowski, who is reported to earn up to €4 million at Dortmund and local police confirmed they have received a complaint on the matter.
Dortmund fans are suspected of carrying out the attack after the Poland striker fell out with supporters when he announced in January that he would be joining rivals Bayern Munich at the end of the season, ending weeks of speculation.
Lewandowski's Dortmund contract expires in June and he leaves for Bayern on a free contract having scored 24 league goals in 31 league games last season, plus 10 in last season's Champions League, as Dortmund lost to Bayern in the Wembley final.
This is not the first time Lewandowski has run into trouble with Dortmund fans. Three weeks ago, he was investigated by police after he was alleged to have struck a teenage Dortmund fan who showed him the middle finger.
Lewandowski is the latest Dortmund player to leave for Bayern after Germany midfield star Mario Götze joined the European champions after actioning a €37 million release clause in his contract last season.