In a piece of political brinkmanship, Prabowo had announced he was pulling out of the final vote count.
"The presidential election process done by the KPU is problematic and not democratic," a combative Prabowo told reporters in Jakarta.
His nephew and a lawmaker in his Gerindra Party, Aryo Djojohadikusumo, told Reuters: "We have withdrawn from the vote tabulation process." He was clarifying earlier comments that his uncle planned to withdraw as a candidate as well.
Allegations of mass cheating
The Prabowo camp alleges mass cheating in the July 9 ballot, enough, they say, to overturn Jokowi's predicted victory.
But unofficial counts suggest that this would require as many as seven million votes switching over to Prabowo, which analysts say is highly unlikely.
Many private counts had given Jokowi a lead of around five percentage points.
The KPU has been widely praised for the way it has conducted the vote in the world's third largest democracy and home to its biggest Muslim population.
"It's reflective of a man who has dedicated the past 10 years to his candidacy," Douglas Ramage, Jakarta-based political analyst, said of Prabowo's reaction to the result going against him. "This was his last shot and ... he has failed to achieve his life's quest. He's disappointed."
The Prabowo camp earlier demanded the commission delay its announcement for two weeks so that the alleged cheating could be investigated.
Confusion over Prabowo's position regarding the election count was enough to rattle Jakarta shares, which had been rising on expectations of a win by Jokowi who is seen as more investor friendly.
At one stage the main index was down two percent on worries that the increasingly shrill dispute could spill over into violence. Prices later recovered.
Read MoreIndonesia stocks surge to 1-year high post election
There have been no reports of major unrest since the election. Hundreds of thousands of police and military personnel are on heightened alert across the vast archipelago of 240 million people.
Companies cancelled events and sent their employees home due to fears of potential unrest, and Jakarta's normally congested roads were quiet at the start of the afternoon rush-hour.
"There are a lot of rumours of instability and unrest, but cautiously I'm confident that it is implausible," said Tobias Basuki, a political analyst at the CSIS think-tank.
Both sides had claimed victory in the closest ever presidential election in Indonesia.
Outgoing President Susilo Bambang Yudhoyono urged whoever loses to quickly acknowledge the outcome to avoid violence.
"Admitting defeat is noble," the president told reporters on Monday, in a clear reference to Prabowo.
Jokowi, born into poverty but now governor of Jakarta, has risen up the political ladder with a clean image and a reputation for competence in local government, in contrast to the autocracy, corruption and power politics that have weighed down the country for decades.
Prabowo's reputation as a strongman and his vow to reverse the indecisiveness of the outgoing government won him a large following among voters yearning for a return to old-style rule.
Candidates can lodge complaints with the Constitutional Court, as did the losers of the previous two elections since strongman ruler Suharto was forced to step down in 1998 after more than three decades in power.
The Court must return a verdict on any challenge within two weeks and it cannot be appealed.
"It is going to take a lot to push this to the Constitutional Court. Prabowo's camp has to prove there was massive, systemic fraud," Basuki said.
Election officials said reports of irregularities had been investigated, but the number of disputed votes is limited to thousands of cases.