Mr Kenyatta won 6,173,433 votes out of a total of 12,330,028. His main rival, PM Raila Odinga, alleged voting irregularities and is expected to file a challenge.
Kenyatta, the son of Kenya's founding president, faces trial after the disputed 2007 presidential vote that unleashed a wave of tribal blood-letting.
If he is declared the winner by the election commission, which has still to announce the official result, Kenya will become the second African country after Sudan to have a sitting president indicted by the International Criminal Court.