The lecturers had been on strike for 18 days.
The state had confirmed that Sh4.77 billion was disbursed to universities and that some staff members had been paid.
Education CS Fred Matiangi said the government had not refused to honour lecturers’ pay rise.
The amount was part of the cumulative Sh10 billion the government awarded three university unions that were pushing for pay rises for members.
They are Uasu, Kenya University Staff Union and the Kenya Union of Domestic, Hotels, Educational Institutions, Hospitals and Allied Workers (KUDHEIHA).
“The three university unions have called off the strike,” UASU secretary general Constantine Wasonga told the press.
Wesonga said the government made new commitments during their negotiations.
He said it was agreed that the CBA “be implemented within this month and that July salaries will have new rates”.
The official said the government also committed to seeing the CBA fully implemented.
“We have signed a return-to-work formula and it has no victimisation,” he said.