The Constitutional Court ruled that there was no evidence of systematic fraud and presidential "meddling", nor that state bodies, regional officials and social assistance had been mobilised to sway polls in the world's third-largest democracy.
"The plaintiff's petition has no legal basis in its entirety," said Chief Justice Suhartoyo, announcing the decision.
Five judges ruled in favour of rejecting the petition, with three dissenting opinions, he said.
Losing presidential candidates Anies and Ganjar Pranowo have both separately alleged there was state interference to favour Defence Minister Prabowo, who won by a huge margin, and had complained his running mate, the current president's 36-year-old son, should not have been allowed to take part.
The administration and Prabowo had rejected the allegations.
The judges are expected to read their decision on Ganjar's petition later on Monday.
The rivals of former special forces commander Prabowo had sought his disqualification arguing the government's widespread distribution of social aid, including handouts of rice, cash and fertiliser, in key areas had swayed the vote in his favour.
Cabinet members in court denied that the aid swayed voters and Prabowo, who won 58% of the vote, has dismissed the claim as baseless.
Judge Saldi Isra, who cast one of three dissenting votes on Monday, agreed that social assistance had been wielded for electoral advantage and argued for a re-vote in some areas.
"Based on the legal and factual consideration, the distribution of social aid... for electoral gains cannot be disregarded at all," he said.
Anies and Ganjar, who won about 25% and 16% of votes respectively, had also alleged that tacit support from the hugely popular President Joko Widodo, better known as Jokowi, had gifted Prabowo an unfair advantage.
Jokowi came under intense scrutiny in the election run-up, with critics alleging he abused his position to favour Prabowo, with the aim of preserving his legacy after a decade in charge of Southeast Asia's biggest economy.
The losing candidates also complained to the Constitutional Court about the inclusion of Jokowi's son Gibran Rakabuming Raka as Prabowo's running mate, which was enabled by a decision in October by the same court to change eligibility rules.
The chief justice at the time was Jokowi's brother-in-law, who was later reprimanded by an ethics panel for allowing intervention from an unspecified "external party". He was barred from involvement in election-related cases.
Despite the ethical violation, the judges said on Monday there was no evidence of nepotism or presidential intervention in relation to that decision.
Former Jakarta governor Anies has warned repeatedly of a democratic backslide in Indonesia, saying the country, which was ruled for 32 years by the late strongman Suharto until his fall in 1998, was at risk of returning to its authoritarian past.
