Uhuru Kenyatta said the security operation is now over after a siege lasting nearly 20 hours left at least 14 innocent people dead.
Police sources and a mortuary official had previously reported 15 were killed in the attack in Nairobi’s upmarket Westlands neighbourhood.
A British man and an American woman who both died have not yet been identified.
Mr Kenyatta said more than 700 civilians have been led to safety after the attack on the DusitD2 hotel and office complex, which includes bars, restaurants, offices and banks.
He did not clarify if people were still hiding on the site.
Mr Kenyatta, who urged Kenyans to “go back to work without fear”, said in a televised address to the nation on Wednesday: “I can confirm that… the security operation at the Dusit complex is over and all the terrorists eliminated.”
He added: “As of this moment, we have confirmation that 14 innocent lives were lost to the… terrorists, with others injured.”
Mr Kenyatta said authorities will “pursue relentlessly” those allegedly involved in the funding, planning and execution of the attack on the hotel complex.
He added that “multiple security efforts are underway to detect, deter, disrupt and defeat any terrorist operative or group.”
Mr Kenyatta added: “From the means available to the security services and judicial arms, we will continue taking every step to make our nation inhospitable to terrorist groups and their networks.”
The Kenyan leader has not confirmed how many attackers were involved in the co-ordinated attack.
Al-Shabaab – the Somalia-based Islamist extremist group that is allied to al Qaeda – claimed responsibility for the deadly siege.
CCTV footage broadcast on local media showed four black-clad, heavily-armed men entering the complex on Tuesday afternoon.
At least one of them blew himself up at the start of the attack.
Authorities sent special forces into the hotel to flush out the gunmen, who local reports said were on the seventh floor of the Grosvenor Hotel.
Video footage from inside the building showed Kenyan security officers searching the premises.
Workers could be seen emerging from hiding places while gunfire could still be heard.
A senior police officer said two attackers had been shot dead on Wednesday morning after a prolonged shootout.
He added: “The two have red bandanas tied around their forehead and bullets strapped around their chest with several magazines each.
“Each had an AK47 which has been secured.”
Sporadic gunfire could be heard from the scene hours before Mr Kenyatta spoke on Wednesday, after scores of people were rescued at daybreak during what police called a “mopping-up” exercise.
Kenyan hospitals appealed for blood donations even as the number of wounded remained unclear.
Al-Shabaab carried out the 2013 attack at the nearby Westgate Mall in Nairobi that left 67 people dead.
Like the attack at the shopping centre, this one appeared aimed at wealthy Kenyans and foreigners.
It came a day after a magistrate ruled that three men must stand trial in connection with the Westgate Mall siege.
Al Shabaab has vowed retribution against Kenya for sending troops to Somalia to fight it since 2011.
Tuesday’s violence came three years to the day after al Shabaab extremists attacked a Kenyan military base in Somalia, killing scores of people.
The group has killed hundreds of people in Kenya.
Al Shabaab claimed responsibility for an assault on Kenya’s Garissa University in 2015 that killed 147 people, mostly students.
The latest carnage demonstrated al Shabaab’s continued ability to carry out spectacular acts of bloodshed despite a dramatic increase in US air strikes against it under President Donald Trump.
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