The defeated candidate, the former general Prabowo Subianto, who also lost Joko in 2014, refused to accept the result and instead declared himself the winner.
Subianto and his campaign accused massive electoral fraud but provided no credible evidence. They did not present a challenge by the Constitutional Court to the outcome of the elections on Thursday as planned, but they have until Friday to do so.
The election supervision agency at the beginning of this week rejected Subianto's complaint about the integrity of the elections after the only proof of fraud provided by his team was the link to online articles.
The uprisings in Jakarta were planned and not spontaneous and many of the hundreds arrested came out of Jakarta, according to the police.
The agents found an ambulance full of stones and other weapons. Some of those arrested had envelopes containing 250,000-500,000 rupees ($ 25- $ 50), Jakarta police chief Argo Yuwono said. The minimum wage in Jakarta is around $ 13 a day.
National police spokesman Muhammad Iqbal told reporters that at least two men detained during the riots belonged to Garis, a militant group that promised support to the Islamic state.
"They intended to carry out jihad during the protests on May 21st and 22nd," Iqbal said.
"This is not a spontaneous incident, this is something of a design," he told reporters.
"There are indications that the mobs are paid and bent to cause chaos."
In a video on his Twitter account late Wednesday, Prabowo urged his supporters to disperse peacefully.
The government has deployed about 50,000 policemen and soldiers in Jakarta. Many residents have left the city and parts of the center are closed to traffic, with the electoral surveillance agency and the Electoral Commission barricaded with barbed wire.