Days of tension gave way to angry scenes as international observers were locked out of the final count and the 76-year-old incumbent confounded early results from Thursday's voting to cling on to power.
At least a dozen people were killed as violence erupted and thousands of opposition supporters took to the streets in the Nairobi slum, Kibera, and the western city of Kisumu. Riots were also reported in Ongata Rongai, Kakamega, the Eastlands district of Nairobi, and Kisii.
Within minutes of the official result, Mr Kibaki was sworn in at a hasty ceremony at State House. While observers and opposition leaders complained of a fix, the President insisted the election had "raised Kenya's democratic profile throughout the world" and set a "good example to the rest of the continent".
The beaten opposition leader, Raila Odinga, who appeared for much of the weekend to be on course for the presidency, accused the electoral commission of "doctoring" the results. "Kibaki has flooded this commission with his cronies and they are putting pressure on the chairman of the commission to announce fraudulent results," he said.
President Kibaki appointed 19 of the 21 electoral commissioners earlier this year. One of the new commissioners is Mr Kibaki's personal lawyer.
International election observers were locked out of the tallying rooms as counting dragged into an unprecedented third day. "They are cooking the books," said one Western observer who had been barred entry.
Koki Mulli, the head of the Institute of Education in Democracy, said: "This is the saddest day in the history of democracy in this country. It is a coup d'etat. It is not about who wins, it is about the legitimacy and the credibility of the process."
Election monitors said the counting process had not been credible. "We have doubts regarding the accuracy of the results," said the chief EU observer, Alexander Graf Lambsdorff.
The opposition Orange Democratic Movement (ODM) claimed there were irregularities in 48 out of the 210 constituencies. In some constituencies the results announced bore little resemblance to those read out in regional tallying centres.
In Molo consitutency, where European Union observers were present, Mr Kibaki won 55,145 votes. When Samuel Kivuitu, head of the electoral commission, announced the result, it had shot up to 75,261. In Kangara, the number of votes for Mr Kibaki rose from 33,835 to 70,443. In Juja it more than doubled from 48,293 to 100,390.
In London, the Foreign Secretary, David Miliband, said Britain had "real concerns" about the result. Mr Miliband tried to speak to Mr Kibaki several times during the day but Mr Kibaki's handlers refused to accept the call.
The announcement of the results by Mr Kivuitu descended into farce as opposition leaders tried to shout him down. Sat in front of a banner proclaiming "free and fair elections", he began to read out results from the disputed constituencies. As ODM leaders arrived they were engulfed in a mêle and one senior party member was hit over the head with a baton by a policeman.
Dozens of paramilitary police officers armed with machine guns and 3ft-long wooden poles moved in and Mr Kivuitu was whisked out. He called on Mr Odinga to take his case to the courts. The High Court in Nairobi has yet to hear cases arising from disputed results from the 2002 election.
"This has taken us back 15 years," said Maina Kiai, chairman of the Kenya National Human Rights Comission, referring to Kenya's first flawed attempt at multi-party elections in 1992. "It is a crying shame. It is very, very painful. This is like Nigeria for crying out loud."
Blogs from the people of Kenya
* Tears are rolling down my eyes as I'm writing this. It is a sad day for Kenya when millions of first-time young voters have had their voice ignored. How do you tell these people their vote matters in 2012?
Kenyan Pundit
* I have just been watching Kibaki being sworn in, amid applause from his cabal. As I sit here in my room, sick to my stomach, and hear the breaking glass outside my house, I ask myself, "What have they done?"
Thinker's Room
* Those who did not know the true character of Mwai Kibaki now do. Moi was better as he handed over power peacefully. One would expect this kind of behaviour from a young President like Kabila of Congo, rather than from this grandfather of almost 80 years old.
Kumekucha
* I stated that, "once the vote has been placed in the ballot box it is next to impossible to do something dodgy." Perhaps I spoke to soon.
Daudi Were
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