Kenyatta who earlier agreed to respect the ruling of the court however made a significant turnaround at a rally in Nairobi where he lambasted judges of the Apex Court.
The recently conducted election was alleged to be fraught with irregularities sparking protests after the election and prompting opposition leader Raila Odinga to go to court.
The court cited irregularities in last month’s election and ordered a new one within 60 days.
The poll had sparked wide protests just as it happened after the 2007 election, however the recent protest was not as violent as the one in 2007 although 28 people died.
Kenya’s election commission had declared Mr Kenyatta the winner by a margin of 1.4 million votes but the result was immediately challenged in court by his nearest rival, opposition leader Raila Odinga.
In a ruling on Friday, Chief Justice David Maraga said the 8 August election had not been conducted in accordance with the constitution, declaring it “invalid, null and void”.
The ruling did not attribute any blame to President Kenyatta’s party or campaign. Mr Odinga, who was in the courtroom, smiled and pumped his fist in the air as the ruling was read out.
Thousands of his supporters took to the streets in celebration. Mr Odinga, 72, said the ruling marked “a historic day for the people of Kenya and by extension for the people of the continent of Africa”.
It is believed to be the first time in Africa that a legal challenge brought by the opposition against a presidential poll result has been successful. Mr Odinga called the electoral commission “rotten” and called for its members to resign and face prosecution.