Kenya's election commission had declared Mr Kenyatta the victor by a margin of 1.4 million votes but the result was immediately challenged in court by his nearest rival, Mr Odinga.
The opposition in Uganda has hailed Kenya's President Uhuru Kenyatta for respecting the Supreme Court's Ruling.
Odinga (right) said the electoral commission as now constituted should not be permitted to conduct the fresh election saying it was complicit in electoral fraud.
The election sparked days of protests, in which at least 28 people were killed. More than 1,000 people died and 600,000 were evicted from their homes in post-election violence that erupted from that election. This time Odinga's supporters at first had said they would not go to court but filed a petition two weeks ago.
"All electoral processes can be improved, and we will continue to support Kenya's institutions in this important work", the statement said.More news: Syrian Army Retakes Uqayribat in Eastern Hama, Kills 120 ISIL Terrorists
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But he also lashed out at the judges, saying "six people have decided they will go against the will of the people".
In order to win the new election, Odinga would have considerable ground to make up.
According to Ruto, the court overturned the will of the the people of Kenya, insisting President Uhuru won the elections fairly.
The Kenyan supreme court, in nullifying the results of the election, cited "irregularities and illegalities" committed by the electoral board that harmed the integrity of the vote.
Kenyatta criticized the court for ignoring the will of the people and called the chief justice's colleagues "crooks".
"They've made one of the most important decisions in Kenyan history", Cheeseman said, "and it's going to be 21 days before we find out why".
The Kenyan electoral commission has been ordered to conduct a fresh presidential election following the provisions of the law within 60 days. Opposition supporters - whose distrust in the voting system appears to have been validated - may see another win for President Kenyatta as proof that the authorities are conspiring against them. Odinga took unsuccessful court action after 2013 elections that he claimed were rigged.