The moves were finalized at an emergency meeting of the school's board of trustees Friday in Chicago.
Trustees chairman Chris Kennedy said he did not fire Hogan, who was hired in 2010 after an admissions scandal and paid $651,000 per year.
Hogan has been heavily criticized by faculty members for his leadership style.
But Kennedy told ABC7's Ravi Baichwal that Hogan was able to streamline some university operations and save money.
"I think it is very difficult to cut $40 or $50 million a year out of an operating budget and to remain popular," Kennedy said.
Long-time administrator Robert Easter takes over July first and will be paid $450,000 a year.