The electoral commission said 7,616,217 valid votes were cast, representing 39% of the voters.
The Supreme Court annulled an August 8 vote at the start of September after opposition leader Raila Odinga challenged the re-election of President Uhuru Kenyatta.
Authorities have banned protests in central Nairobi in a bid to keep a lid on mounting political turmoil in the build-up to the repeat vote.
On September 1, the Supreme Court nullified incumbent Kenyatta’s win due to procedural irregularities and ordered a new election.
Last month, Kenya’s Supreme Court voided the August 8th presidential election, citing irregularities, but did not criticise any specific individual.
The key finding against the election board on Wednesday was that officials had announced results before being able to verify them.
The election will feature Kenyatta, who is running for a second term, and opposition leader Raila Odinga, the commission said.
David Maraga’s declaration that the August 8 election was void and demand for a new poll with 60 days shocked many in the East African nation and abroad.
The decision to cancel the vote result, the first of its kind in Kenya’s history, sets up a new race for the presidency between Kenyatta and veteran opposition leader Raila Odinga.
Election authorities say Kenyatta won a second term in the August 8 polls by 1.4 million votes. A parallel tally by independent monitors based on a sample of around 2,000 polling stations produced a similar result.
The Kenya Communication Authority’s new media regulations have raised worries about the government trying to control coverage of the polls.