President Joko Widodo appealed for calm after two suicide attackers unleashed carnage outside the busy terminal late Wednesday, sending huge clouds of black smoke into the sky and panicked people fleeing.
Three policemen were killed, while six other officers and five civilians were injured in an assault that left body parts and shattered glass strewn across the road. The bombers also died.
Police said they believed there was a link between the attackers and the ISIS, without giving further details. Hundreds of Indonesians have flocked abroad to fight with the jihadists and ISIS-supporting militants have been behind a series of recent plots and attacks in the archipelago.
The bus station bombing was the deadliest attack in Indonesia since January 2016, when a suicide blast and gun assault claimed by ISIS in downtown Jakarta left four attackers and four civilians dead.
In a televised address Thursday, 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 and their families -- especially the police officers who passed away while performing their duty," he added.
The main investigation was handed over early Thursday to the police's elite anti-terror squad Densus 88, which has played a leading role in tracking down and killing some of Indonesia's most wanted militants.
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.
Security forces have been the main target in recent years of Indonesian militants, who have largely turned their attention away from Westerners.
Suspicion is likely to fall on local network Jamaah Ansharut Daulah (JAD), which supports IS and has been blamed for recent, mostly low-impact, attacks.
The bombs used in Wednesday's attacks were made from pressure cookers, similar to a device used in an attack by a JAD militant in the Indonesian city of Bandung in February.
Another police spokesman, Setyo Wasisto, added terror cells "might have been inspired to carry out an attack" by recent assaults in Britain and the Philippines.
Twenty-two people, including children, were killed when a suicide bomber attacked a pop concert in Manchester on Monday. In the Philippines, troops are locked in intense battles with Islamist militants who rampaged through the mainly Muslim city of Marawi.
Police said the first bomb in the latest Jakarta attack was detonated at 9:00 pm (1400 GMT) in an area where police officers were on duty. Five minutes later the second bomber struck about 10 metres (32 feet) away.
Local media said the event that the officers were preparing to guard was a torch parade traditionally held before the Islamic holy month of Ramadan, which begins this weekend.
The Kampung Melayu terminal is a local hub served by minibuses and buses.
Indonesia has long struggled with Islamic militancy and has suffered a series of attacks in the past 15 years, including the 2002 Bali bombings that killed 202 people, mostly foreign tourists.
A sustained crackdown weakened the most dangerous networks but the emergence of ISIS has proved a potent new rallying cry for radicals.