Five officers and five civilians were wounded.
Eight people were killed in that attack, including the militants.
Hundreds of radicals from the Southeast Asian state have flocked to fight with IS, sparking fears that weakened extremist outfits could get a new lease of life.
It is suspected that was only one suicide bomber involved but that he had also placed another bomb in the area which went off during the attack, leading to the two blasts that witnesses cited, Wasisto said.
News outlet Detik.com reported the police had confiscated bayonets, military equipment, official documents including passports and a marriage license and books on religion during the raid.
"This is execrable. Ojek (motorcycle taxi) driver fell victim, public minivan driver, store sellers, as well as policemen", Joko told reporters in his hometown in Central Java, referring to the three slain police officers and 11 others injured, the presidential palace said in a statement. The bombings on Wednesday night also injured five other police officers and five civilians.
According to sources within Jakarta's Police Department, the terrorist made use of homemade pressure cooker bombs.
Evidence found at the crime scene included nails, metal parts and a receipt for a pressure-cooker.
A member of the police bomb squad inspects the site of an explosion in Jakarta, Indonesia, Wednesday, May 24, 2017.
National police spokesman Setyo Wasisto said he was deeply concerned about the events following the attacks in Manchester and Philippines.
The terminal may have been targeted for its increased police presence, with extra officers deployed ahead of a torch rally to celebrate the start of the Islamic holy month of Ramadan, authorities said.
"There were two blasts at around 9 p.m., close to each other", Wibowo told the local MetroTV station.
Hundreds of Indonesians have flocked overseas to fight with the armed group in Syria and Iraq, and ISIL-linked combatants have been accused of being behind a series of recent plots and attacks across Indonesia.
The attack comes just days after the suicide bomb attack at Manchester Arena in the United Kingdom that killed 22 people.
If the perpetrators were connected to the Bandung bombing, it is possible that the motive behind the Jakarta attack was similar: for the police to release prisoners held by Indonesian counterterrorism forces. Australia and Indonesia plan to jointly host an Asia-Pacific summit in August aimed at coordinating against the security threat posed by homegrown Islamic militants returning from battlefields in Syria and Iraq.