However, he immediately disputed reports that Widodo was in the lead and claimed to have won 55.4 per cent of the vote in exit data collected from 5000 polling stations.
He alleged that "many ballots were not delivered to the polling stations, many polling stations were opened [late] at 11am. There were many anomalies".
The presidential race was a rematch of the 2014 contest when Prabowo claimed victory on election day, before contesting the results at the Constitutional Court, which confirmed Widodo's win.
The delay in issuing the official results is a reflection of the vast logistical operation behind holding a presidential and parliamentary election on the same day across three time zones and an archipelago of about 17,000 islands.
More than 192 million Indonesian voters were eligible to cast their ballots for a record 245,000 candidates.
Analysts suggested there was not a huge variation between the economic agendas of the two leading presidential nominees, leading them both to lurch to the right to court conservative Islamic forces in an effort to garner more votes.