The toll was confirmed by Jakarta Governor Anies Baswedan, while police sources told Efe news that at least 60 people had been arrested.
In the protests that began on Tuesday night and continued into Wednesday morning, demonstrators who had gathered outside the headquarters of the Elections Supervisory Agency and the Election Commission burned several vehicles after the police tried to disperse them with tear gas.
The violence broke out at the end of a peaceful protest held by supporters of the defeated presidential candidate Prabowo Subianto, who has said he will challenge the election results in the Constitutional Court, citing electoral fraud.
Some 32,000 officers are guarding the headquarters of the two election bodies with barbed wire and riot vehicles ahead of more potential protests later on Wednesday.
National Police spokesperson Dedi Prasetyo said that some 1,300 people who had travelled to Jakarta were staying in mosques with the intention of continuing the protests.
Authorities have also warned of possible terror attacks and have arrested dozens of radicals who were allegedly planning attacks during the demonstrations.
The protests came after the Election Commission on Tuesday confirmed Joko's outright victory in the April 17 general elections, in which he secured 55.5 per cent of the ballots against 44.5 per cent for Prabowo, who has refused to recognize or validate the final result of the polls.
On Monday, Indonesia's Election Supervisory Agency rejected claims by Prabowo's camp of "structured, systematic and massive election administration violations", although it did identify certain small-scale irregularities with the management of ballot boxes by election officials.
( With inputs from IANS )