As counting began after a day marked by bloodshed and poor voter turnout yesterday, President Uhuru Kenyatta was heading for a landslide victory after his rival Raila Odinga pulled out.
But estimated figures compiled by the election board pointed to a turnout of just 48 percent.
If confirmed, it would be a huge fall from the nearly 80 percent rate in the August poll, which was won by Kenyatta but overturned by the Supreme Court in an unprecedented ruling that sparked weeks of protest and acrimonious debate.
The confirmed casualties raised the number of people killed in election-related violence since the August poll to 44.
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In a televised address after the polls closed at 1400 GMT, election chief Wafula Chebukati said eight out of 10 of the country's polling stations had opened.
"We have 40,883 poll stations... out of that number, 35,564 polling stations opened or sent an opening message, meaning voting took place and this is representing 87 percent of polling stations," he said, noting there were 5,319 that did not open or were unable to send an opening message.
But Kisumu's governor Anyang Nyongo rejected the move, saying people would not vote while they were "mourning".
While Odinga's supporters hit the streets, others went to the polls to cast their ballots.
But, in stark contrast to the August election, several polling stations in key areas stood empty or welcomed only a handful of voters in an election likely to face more legal battles after its conclusion.
At one polling station in Nairobi's Kibera slum, rocks bounced off the roof as officials tallied just 16 votes -- all for Kenyatta.
As voting headed to a close, police and hospital sources confirmed four people had been shot dead and around 50 others wounded, most by live bullets, according to an AFP tally of figures from officials and medics.
At the Jaramogi hospital in Kisumu, an AFP correspondent saw several people arriving covered in blood.
"This is crazy, they are shooting at us -- we are demonstrating and they shoot us!" said Samuel Okot, 20, who was sitting with his friend Joseph Ouma who had been shot in the knee and was howling in pain.
The violence drew a sharp response from rights watchdog Amnesty International.
"With tensions running high there is a very real threat of further bloodshed as the election re-run takes place," said Justus Nyangaya, director at Amnesty International Kenya.
"We are calling on the police to only use force as a last resort -- unlawful police killings and other human rights violations must not be allowed to recur."
In Kisumu, 19-year-old George Odhiambo died from blood loss after being shot in the thigh during clashes which erupted after protesters barricaded roads and polling stations to block the vote, police and hospital sources said.
Police said another man was shot dead in Homa Bay, also in the west, "where a large mob attacked a small police facility" prompting officers to open fire "to protect themselves", a statement said.
A fourth man died after being shot in the head in Nairobi's Mathare slum, another hotspot in the capital where police fired water cannon and teargas to disperse demonstrators.
In the eastern port city of Mombasa, police said a man was stabbed as he was going out to vote, while in Kisumu a police officer was also wounded with a knife.