Outside the Nairobi court, Kenyatta supporters waved Kenyan flags and danced, and celebrations broke out in the central city of Nyeri, a ruling party stronghold, and other cities.
In the western, pro-opposition city of Migori, protesters said one person was killed in skirmishes with the police after the court ruling.
Migori county police commander Joseph Nthenge denied the report.
There were no deaths reported from Kisumu, the largest city in western Kenya and a hotbed of opposition support, although police and protesters also briefly clashed there too.
In the Nairobi slum of Kibera, residents said three people were killed on Monday, including a 67-year-old woman and a young man, but there were conflicting reports of who was responsible for the violence.