The teenager filed a complaint with police saying Lewandowski, who earlier this month agreed to join treble winners Bayern next season, had punched him on the forehead on Thursday.
"I want to clearly state that I never used violence against people who violated my private sphere," the Poland international said in a statement on his Facebook page.
The teenager has admitted to making an offensive gesture as the player drove by in his car near his home in Dortmund.
Lewandowski, whose move has angered Dortmund fans after Mario Goetze also left to join the Bavarians this season, stopped the vehicle and got out to confront the 17-year-old.
"I have no intention of teaching teenagers how to behave but I will not allow for my family and myself to be offended," Lewandowski said.
Club officials backed the player.
"Robert swears he never hit the boy in the face and that he never even touched him," Dortmund CEO Hans-Joachim Watzke told Bild newspaper.