At 9pm local time, the first bomb exploded near the bus terminal.
A suspected suicide bombing at a bus terminal in Jakarta has killed three police officers and injured five others, Indonesia's deputy police chief says.
He said that although further investigation is needed to disclose more details of the attack, it can be confirmed that it was "a two-man suicide show with two blasts in overlapping time and location". Hundreds of Indonesians have flocked overseas to fight with the jihadists and IS-supporting militants have been behind a series of recent plots and attacks in the archipelago.
In a televised address, President Joko Widodo said he had ordered a thorough probe and was "urging all citizens across the nation to stay calm and remain united".
"I convey my deepest condolences to the victims' families. especially to the policemen", he said in a statement.
Mr Setyo said police were still investigating whether the blasts were linked to recent attacks around the world.
Police believe they were specifically targeted in the bombing as they prepared to provide security for a parade near the Kampung Melayu terminal, which is an area frequented by locals but not foreigners.
The elite police squad Densus 88, which has played a leading role in tracking down and killing some of Indonesia's most wanted fighters, is now taking the lead in the investigation.
The man was married with two children and used to work as a herbal medicine seller, said the spokesman. He also said there was a strong smell after the blasts. He said the victims were taken to several hospitals.
"There's a link, but we're still studying whether it's an global network", said National Police spokesman Awi Setyono, who told reporters earlier that police are investigating whether the attackers had direct orders from Syria or elsewhere.
Wednesday saw two explosions at approximately 9 p.m. and 9.05 p.m., which caused the deaths of three police officers and two alleged suicide bombers.
The Department of Foreign Affairs and Trade upgraded its travel advice on Thursday, warning Australians in Indonesia of an ongoing high threat of a terrorist attack.
The most recent terrorist attack in Jakarta, prior to Wednesday, was on Jan 14, 2016, when the capital was rocked by multiple explosions, including one at a police post, and gunfire around the Sarinah shopping mall in Central Jakarta. Five minutes later the second bomber struck about 10 metres (32 feet) away.
Police patrol near the scene of an explosion at a bus station in Kampung Melayu, Jakarta, Indonesia May 25, 2017.