Jarstein was unable to contain his frustration after conceding a 96th-minute equaliser and angrily kicked the ball away after Robert Lewandowski's goal, hitting Xabi Alonso in the process.
Bayern players reacted furiously to the incident and Neuer feels the 32-year-old set a bad example with his unsporting behaviour.
"It is just not right to shoot the ball at a player on purpose, no matter how frustrated you are," Neuer told the German Football Association website. "It is about fairness.
"It does not set a good example as a role model. The stadium was sold out and many viewers were watching the game on TV.
"I think it was understandable that we complained about that."