Indonesian presidential election challenger Anies Baswedan filed a complaint to the country's Constitutional Court on Thursday contesting Defense Minister Prabowo Subianto's decisive win after allegations of irregularities and fraud.

Prabowo, 72, was confirmed as the next leader of the world's third-biggest democracy on Wednesday, beating former Jakarta governor Anies and a third rival with 58.6 percent of the vote -- enough to secure a first-round majority.

But the campaign was mired in allegations that outgoing leader Joko Widodo, more popularly known as Jokowi, had interfered in a bid to establish a political dynasty, as his eldest son Gibran Rakabuming Raka ran as Prabowo's vice president.

"We officially submitted the request for an election dispute petition to the Constitutional Court," Anies's legal chief Ari Yusuf Amir told reporters outside their campaign headquarters. 

"Earlier this morning at 1:00 am (1800 GMT Wednesday), we submitted the registration online, and currently our team is at the Constitutional Court processing the administrative requirements."

Anies's team has said the aim of the complaint is to improve future elections and Indonesia's young democracy, which emerged from decades of autocratic rule in the late 1990s.

Jokowi was criticized after his brother-in-law, then-chief justice Anwar Usman, issued an October ruling lowering the age requirements for presidential and vice presidential candidates that allowed Gibran to run with Prabowo.

Anies -- who got 24.9 percent of the vote -- refused to concede after official results were announced Wednesday, condemning the winner's route to victory.

"Leadership that was born out of a process tainted by cheating and violations will result in a regime that will produce policies that are full of unfairness, and we don't want this to happen," he said in a statement.

Anies's running mate Muhaimin Iskandar said Wednesday evening that alleged irregularities included "regulatory engineering to the intervention of state apparatuses".

Prabowo was widely predicted to win the presidency on his third attempt after losing in 2014 and 2019. 

His legal team was confident the result would not be successfully challenged because of his majority and wide margin of victory, local media reported. 

Officials from his campaign team did not respond to an AFP request for comment.

He takes over in October after a transition period.