The Independent Electoral and Boundaries Commission (IEBC) has, however, explained that this was caused by a delay in completion of paperwork.
Through its Twitter handle, IEBC stated that Joho was set to receive his certificate on Saturday at 2 pm.
"Our Mombasa County RO did not refuse to give the Governor elect certificate. Paperwork took long, both parties agreed on 2 pm today (Saturday)," it stated.
Unlike other counties nationwide, final results from the Mombasa governor election are yet to be declared despite Joho having taken an unassailable lead.
Mombasa County Returning officer Nancy Kariuki said they were still verifying results from various polling stations in the county.
Preliminary results showed that Joho was leading with 220,576 votes against Jubilee Party's Suleiman Shahbal who got 69,322 votes. Senator Hassan Omar who was vying on a Wiper Party ticket garnered 43,672 votes.
On Friday, Joho questioned why the presidential results were declared before his.
"How can they declare the presidency, it means Mombasa may not have been factored in," the Governor lamented.
Joho claimed the state was delaying declaring results to push him to the wall and force his supporters to the streets.
He, however, asked his supporters to remain peaceful adding that he was ready for another election if IEBC denied him a certificate.
During the announcement of presidential results at Bomas of Kenya, IEBC Chairman Wafula Chebukati noted that Mombasa County had no spoilt votes.