However, supporters of his main rival, PM Raila Odinga, have alleged voting irregularities and indicated he would file a legal challenge.
Violence after the 2007 election left more than 1,000 people dead.
The IEBC said the latest elections had been complex and difficult but also credible and transparent.
It said the turnout was the largest ever.
IEBC chairman Issack Hassan said that Kenyans had voted "calmly, patiently, proudly and peacefully in the full glare of whole world".
However, one of Mr Odinga's aides said earlier that the candidate had "no intention" of conceding defeat.
Salim Lone told the Daily Nation newspaper: "The level of the failures in the system makes it very difficult to believe it was a credible result."
Both candidates have complained of irregularities during the course of the count, since Monday's election.
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