Hundreds of Hamas fighters had moved on the positions after giving their occupants two hours to leave.
Three Hamas fighters were killed, two of whom were involved in rocket attacks.
They said Hamas fighters were shooting from the buildings and storing weapons at the university.
It has provided money and training for Hamas fighters.
Israel also claimed that many Hamas fighters were killed.
A gunfight broke out, in which one Hamas fighter was killed.
The Israeli military said that 50 Hamas fighters were killed and dozens more wounded.
The Israeli military said that 80-100 Hamas fighters were killed and 100 captured during heavy ground fighting.
It was reported that Hamas fighters had been ordered not to wear military uniforms during the fighting.
Fatah said that Hamas fighters were using the university as a base for attacks on nearby police stations.