Lecturers are returning to work because the government had deposited money into a development fund for campuses, union leaders said.
The government had initially pledged to spend $1.3bn ($800m) to refurbish badly maintained public universities.
Nigeria is Africa's main oil producer, but its infrastructure is poor.
Education Minister Ezenwo Nyeso had threatened to dismiss lecturers who failed to return to work by 4 December.
However, members of the Academic Staff Union of Universities (ASUU) defied the ultimatum, continuing with the strike until it was called off on Tuesday.
