The unanimous decision to reject the petition in effect ends the political aspirations of controversial retired general Wiranto, a close confidant of former president Suharto who has been accused of numerous human rights violations.
"I accept the decision of the constitutional court," Wiranto said.
His lawyers had argued that ballot irregularities cost his candidacy more than 5.4m votes, which would have been sufficient to put him in second place in the first round run-off of presidential elections, ahead of incumbent president Megawati Sukarnoputri.
Only the top two candidates advance to the final round.
On election day, officials ordered a recount of tens of millions of ballots after it was discovered that many voters had failed to unfold their ballots completely, inadvertently punching them twice.
The decision clears the way for the 20 September final-round race between Megawati and another retired general, former security minister Susilo Bambang Yudhoyono.
President Megawati (R) is said to
be relieved by the decision
"We're relieved," Megawati adviser Trimedya Panjaitan told the online news service detik.com.
"Statements made by the head of the court created big questions and frankly we were worried. We think that... it would be better during [future] elections if the constitutional court only accepts requests that are accompanied by strong evidence, not like this one."
Wiranto returned to the public eye in late 2003 after being dismissed from the cabinet of Abdurrahman Wahid, the nation's second post-Suharto president, two years earlier.
He was indicted by a UN-supervised court in East Timor for human rights abuses.
As many as 2000 residents of the former Indonesian province are believed to have died when pro-Jakarta militias backed by Indonesian security forces ran amok after the population voted in favour of independence during a UN-sponsored referendum.
Wiranto was head of the armed forces at the time.
The 57-year-old native of Central Java was courted by a faction of Suharto's ruling Golkar Party and in April beat its influential chairman Akbar Tanjung to become the party's presidential candidate.
The battle between the two men revealed deep divisions within Golkar, and there was widespread speculation during the first round of the presidential elections that behind the scenes Tanjung was attempting to undermine Wiranto's efforts.
"If Wiranto doesn't make it to the second round of the elections he's finished," Northwestern University professor Jeffery Winters predicted. "In that sense, the results of the elections will decide the results of the struggle within the party."
This is the second high-profile case involving the newly formed constitutional court in the past two weeks. Observers say it is one of the few elements of Indonesia's notoriously corrupt justice system that has not been tainted by accusations of bribery and corruption.
The court last month ruled unconstitutional the tough anti-terrorism laws used to detain and later imprison dozens of suspects in a series of bombings in Indonesia.
Bashir (C) could be released
after the court precedent
In October 2002, members of Jemaah Islamiya, a homegrown group with alleged links to al-Qaida, detonated two bombs in Bali's nightclub district killing more than 200 people, many of them foreign tourists.
It stands as the bloodiest bombing since the attacks on New York city and Washington DC a year earlier.
The court decided by a 5-4 margin that the laws which were drafted in the wake of the Bali bombs could not be applied retroactively.
The decision, hailed by legal experts abroad as a promising sign of judicial independence in Indonesia, has been attacked at home by the victims of the violence, with a series of loud demonstrations on the resort island in recent weeks.
Lawyers for some of those convicted of involvement in the attacks say they are afraid they will be attacked if they return to Bali to file their appeals.
Thirty-two people have been convicted of involvement in the Bali attacks. Three have been sentenced to death while the rest are serving sentences ranging from three years to life imprisonment.
Lawyers representing controversial Muslim cleric Abu Bakr Bashir, who Western intelligence services have called the spiritual leader of a violent movement to create a pan-Asian Islamic state, say they plan to use the court ruling to argue for his release.
The decision could also affect the cases of more than a dozen men convicted of involvement in the truck bomb that blew up outside the US-owned Marriott hotel in downtown Jakarta last August killing 12.
The ring-leaders of both the Bali and Marriott hotel bombings are still at large.