The 25-year-old Lewandowski, who will leave Dortmund to join rivals Bayern Munich in July on a free transfer, is said to have struck the youth, but denies the allegation.
“I would like to clearly state that I used no force against any persons who invaded my personal space,” Lewandowski wrote on his Facebook page.
“I do not intend to teach teenagers how to behave.”
Lewandowski said the incident happened near his home.
“We have received a complaint of assault concerning a player from Borussia,” a police spokesman confirmed to German daily Bild.
Two witnesses have verified the incident.
The teenager said he saw Lewandowski drive past his Dortmund school in a Porsche Cayenne and showed the star his middle finger in his frustration at the Bayern move.
“I know it wasn’t right,” the teenager told Bild.
“But he jumped out of the car and stormed towards me like a bull.
“He said to me ‘what was that, what did you do?’, then struck me on the forehead with the palm of his hand, I flew backwards.”
Dortmund CEO Hans-Joachim Watzke backed the player.
“I have spoken with Robert Lewandowski and he explained that the boy showed him the middle finger,” said Watzke.
“Then he got out of the car, put his hand on the boy’s shoulder and asked him why he was doing such a thing.
“Robert swears that he did not touch his face or hit him, I believe Robert 100 percent.”
Lewandowski scored 24 goals in 31 Bundesliga games last season and has already netted 11 times in 17 league appearances so far this season.