The criminal complaint says the 25-year-old Lowry was taunting 30-year-old Infini Robinson while she was officiating a game between NBA players Sept. 22.
Police say that when the game ended, he threw a ball at her torso and cursed at her for calls he didn't agree with.
Robinson later was hit in the shoulder by another basketball in an area designated for officials. She said the ball hit her with such force that it pushed her body back in the chair where she was sitting, and said it likely would have broken her nose had she not been bent over changing her shoe.
The report says Corey Maggette of the Charlotte Bobcats approached her afterward and apologized on behalf of Lowry. She told police Lowry also approached her, saying "I truly apologize for what I did. I let my emotions get the best of me."
Lowry could not be reached by phone Friday. He was in the training room prior to the Rockets' game Friday night at Oklahoma City and was replaced in the starting lineup by Goran Dragic because of a right foot injury.
Lowry had started Houston's first six games and is averaging 15.3 points and 10 assists, the third-best total in the league.
Rockets general manager Daryl Morey says he is aware of the complaint but is not commenting on the legal matter.
Lowry has been summoned to appear in a Las Vegas court Feb. 2.