A 17-year-old filed a complaint with police alleging Lewandowski, who earlier this month agreed to join Bayern in the summer, 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 official Facebook page.
The teenager has admitted to making an offensive gesture as the player was driving near his home in Dortmund.
Lewandowski, whose move has angered Dortmund fans after Mario Götze also left to join Bayern last year, stopped the vehicle and got out to confront the teenager.
"I have no intention of teaching teenagers how to behave but I will not allow for my family and myself to be offended," Lewandowski added.
Dortmund backed their player with CEO Hans-Joachim Watzke telling reporters, "Robert swears he never hit the boy in the face and that he never even touched him."