Assistant coach Bob Cantu will serve as interim head coach while the university searches for a successor.
Haden said in a statement that it became evident to him this season that the program needed new leadership and that it was best to make the change now to "re-energize" the team.
O'Neill was in his fourth year with an overall record of 48-65. The trojans are 7-10 this season.
The Associated Press contributed to this report.