The challenge had been widely expected, but many analysts believe it would be near impossible for Mr Prabowo to overturn the result of the election, seen as among the cleanest in the country's history.
The losers in the previous two presdiential elections also went to the court to raise objections, but to no avail.
The head of Prabowo's legal team, Mahendradatta, said: "We have decided to bring this case to the Constitutional Court (within three days)."
He estimated there were about 21 million disputed votes out of the total of around 130 million. Jakarta governor Joko "Jokowi" Widodo was declared the winner on Tuesday with 53.15 per cent of the vote. He won by nearly 8.5 million votes.
As the final vote count neared, and Jokowi's victory looked increasingly certain, the Prabowo team raised charges of widespread cheating and accused the Elections Commission of not properly investigating the allegations.
Constitutional Court Secretary General Janedjri Gaffar said if the suit is filed by this weekend, the case would be heard from August 6 and a verdict delivered by August 21.