Jokowi's final tally was put at 53.15 per cent, according to one report, and party chairwoman Megawati Sukarnoputri said: "I want to declare that we, the party that supports and puts forward Joko Widodo and Jusuf Kalla (for vice president), has won." Jokowi will take office in October to serve a five-year term.
But in a piece of political brinkmanship, the man expected to come second, former general Prabowo Subianto, said he was pulling out of the final vote count.
The move will have no impact on the result, but it does suggest the former special forces commander could take his fight to the Constitutional Court.
Mr Prabowo said: "The presidential election process done by the KPU is problematic and not democratic."
The Prabowo camp alleges mass cheating in the July 9 ballot, enough, they say, to overturn Jokowi's predicted victory.
But unofficial counts suggest this would require as many as seven million votes switching over to Mr Prabowo, which analysts say is highly unlikely. Many private counts have 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, a Jakarta-based political analyst said of Mr 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. Both sides had claimed victory in the closest ever presidential election in Indonesia.