He narrowly beat his rival, Raila Odinga, taking 50.5% of the vote, according to the official results.
The announcement was delayed amid scuffles and allegations of vote-rigging by Mr Odinga’s campaign.
Four of the seven members of the electoral commission refused to endorse the result, saying it was “opaque”.
“We cannot take ownership of the result that is going to be announced because of the opaque nature of this last phase of the general election,” said Juliana Cherera, the vice-chairperson of Independent Electoral and Boundaries Commission (IEBC).
“We are going to give a comprehensive statement… and again we urge Kenyans to keep calm. There is an open door that people can go to court and the rule of law will prevail,” she said.
Mr Odinga’s party agent earlier alleged that there were “irregularities” and “mismanagement” in the election.
This was the first time Mr Ruto, 55, had run for president. He has served as deputy president for 10 years, but fell out with President Uhuru Kenyatta, who backed Mr Odinga to succeed him.
The 77-year-old former prime minister was running for president for the fifth time.
The electoral commission chairman Wafula Chebukati said he had done his duty despite receiving threats.
“We have walked the journey of ensuring that Kenyans get a free fair and credible election. It has not been an easy journey – right now two of my commissioners and the CEO are injured,” he said.
In his speech, President-elect Ruto thanked the electoral commission for overseeing the election.
“It is a wonderful evening… all sovereign power belongs to the people of Kenya,” Mr Ruto said, calling Mr Chebukati a “hero”.
Mr Ruto said he wanted to be a president of all, and for the country to focus on the future.
“To those who have done many things against us, I want to tell them there’s nothing to fear. There will be no vengeance. We do not have the luxury to look back,” he added.
Celebrations have broken out in several parts of the country including in Mr Ruto’s strongholds of the Rift Valley, and that of his deputy Rigathi Gachagua, in the Central region.
Supporters of Mr Odinga have staged small protests in the western city of Kisumu and some parts of Nairobi.