The opposition leader, Raila Odinga, pulled out of the re-run and urged his supporters to boycott it.
Mr Kenyatta was also declared the winner in the August vote, which was annulled because of “irregularities”.
The re-run was suspended in 25 constituencies amid security fears. The commission said those results would not affect the final outcome so it could proceed with its announcement.
Commission chairman Wafula Chebukati described the latest vote as “free, fair and credible”.
Kenya’s opposition now has seven days to mount a legal challenge, and Mr Odinga says he will make an announcement on Tuesday.
About 50 people are reported to have died in violence since Mr Kenyatta was declared the winner in August’s election.
Mr Odinga had wanted the repeat ballot to be held at a later date, but a bid to delay the election re-run fell apart after only two of seven Supreme Court judges attended a hearing last week.
It’s not over yet
By Alastair Leithead, BBC News, Nairobi
There was a sense of relief, as well as déjà vu, at the national tallying centre, when the chairman of the electoral commission said Uhuru Kenyatta had won the presidential election – this time with a little over 98% of votes.
Kenyans are tired of political wrangling, legal challenges, and repeated elections, but it’s unlikely this will be the end of the matter.
Opposition leader Raila Odinga, who called on his supporters to boycott the ballot, is expected to reject the result – given the low turnout and continuing legal challenges.
The Supreme Court still has to consider a petition questioning the legitimacy of the poll, and given the ambiguities over electoral law and the way the constitution is interpreted, further legal arguments are expected.
There have been violent clashes between opposition supporters and police in parts of Nairobi and western Kenya and how Raila Odinga takes this defeat will determine Kenya’s path over the coming days and weeks.