IEBC declared Uhuru the winner on August 11 with a 54 per cent against Raila's 44 per cent, hence avoiding a runoff.
But Raila Odinga, in the 25,000-page presidential petition, accuses the electoral agency of manipulating votes in favour of Uhuru and denying him the win.
The petition, delivered by a battery of lawyers, was received at the highest court in the land at around 11.30pm by registrar Esther Nyaiyaki.
Nyaiyaki, being satisfied that the petition has met all the requirements, allowed it to proceed to the next stage.
It cost the opposition Sh1.7 million to file the suit. Court officials assessed the voluminous documents ahead of the Friday midnight deadline.
The documents, which were transported to the court in a truck, were drawn by Murumba and Awele Advocates.
NASA principals Raila and Kalonzo Musyoka are the petitioners.
The three respondents are IEBC, commission chair Wafula Chebukati and President Kenyatta.
Musalia Mudavadi, and Moses Wetang'ula were present at the time of the filing.
Scores of NASA supporters camped outside the Supreme Court building in wait for the filing of the petition.
The placard waving supporters waited patiently till late into the night as NASA lawyers prepared the case documents.
The Supreme Court Registry remained open past the 8am-5pm working hours to accommodate the petition.
"Uhuru must go! Uhuru must go!" the NASA backers chanted.
Raila also challenged Uhuru's election in 2013 but the case was dismissed by a bench chaired by former CJ Willy Mutunga.
Although he accepted the outcome, Raila said he did not agree with the judges decision.
Scores of anti-riot police were deployed outside the building to keep watch.
Raila unveiled his petition plan during a press conference on Wednesday, after going back on his word that he would not got to court.
He has two days to serve respondents with the suit papers.
Chebukati will have four days to file responses and attempt to dismantle the allegations lodged by the opposition.
Parties will converge in court on the seventh day for an interlocutory application where they are expected to frame contested and uncontested issues in the petition.
Other parties wishing to join the case will apply to be enjoined.
On the eighth day, parties will have a pre-trial conference where together with the court, they will agree on how the hearing will proceed.
The Supreme Court decision must be delivered on September 1.
It will be heard by Chief Justice David Maraga, judges Mohamed Ibrahim, Prof Jackton Ojwang’, Dr Smokin Wanjala and Lady Justice Njoki Ndung’u.
Apart from Maraga, the other judges arbitrated the 2013 petition and will now be joined by deputy Chief Justice Philomena Mwilu, and Justice Isaac Lenaola.
-The Star