The commission said Kenyatta won Tuesday's election with 54 percent of the vote.
The announcement of the results was delayed for hours, after election officials said they needed time to review some documents from some polling districts.
NASA had repeatedly complained that there were anomalies in the results that IEBC was streaming on its portal and wanted them audited before a final result could be announced.
At least three deaths were reported in the days between the election and the announcement of the results Friday night as opposition supporters protested and clashed with police.
"But sadly, we have seen violent protests, in which property has been damaged, and lives have been endangered", he said. It is my hope that during your second term in office, we shall continue to work together towards strengthening the friendly relations between our two nations. As with any competition, there shall always be winners, and there shall be losers.
UN Secretary-General Antonio Guterres urged Odinga to "send a clear message to hissupporters urging them to refrain from violence", a message echoed by UK Foreign Secretary Boris Johnson.
The eruption of violence has revived memories of a decade ago, when Odinga, now 72, lost an election in controversial circumstances that sparked a wave of political and ethnic unrest in which 1,200 people were killed and 600,000 displaced.
In 2007 an opposition coalition led by Odinga disputed the result after incumbent Mwai Kibaki was announced the victor by the electoral commission.
Police, who were deployed in anticipation of the results, have fired tear gas in several locations, fires have been lit by protesters on a road in the heart of Kisumu and gunshots have also been heard, a BBC reporter says.
Opposition official James Orengo later called the election process a "disaster".