Police chiefs across the country were on high alert, some embassies in Jakarta were closed for the day and security was stepped up on the resort island of Bali, a draw for tourists from Australia and other Asian countries.
“It's clear that the (Jakarta attackers) didn't set this up themselves. For this, we are searching for the networks and who was involved in this action,” said Anton Charliyan, national police spokesman.
Security forces killed what they said was one suspected militant in a gun battle in Central Sulawesi, while two others were arrested in the city of Cirebon in West Java.
The three were believed to be ISIL supporters, but not directly connected to the Jakarta attack, police said.
Returning to the area outside Jakarta's oldest department store, Sarinah, where Thursday's attack unfolded, the city's police chief said the rise of ISIL was a cause for serious concern.
“We need to strengthen our response and preventive measures, including legislation to prevent them … and we hope our counterparts in other countries can work together because it is not home-grown terrorism, it is part of the ISIS network,” Tito Karnavian said, using another acronym for the Syria-based group.
In response to the Jakarta attacks, Philippine President Benigno Aquino ordered security forces to strengthen defenses of “soft” targets. Malaysia placed the country on its highest alert.
Experts agree that there is a growing threat from radicalized Muslims inspired by ISIL, some of whom may have fought with the group in Syria.
However, they said the low death toll on Thursday pointed to the involvement of poorly trained ISIL supporters whose weapons were crude.
An Indonesian and a man of dual Canadian-Algerian nationality were killed along with the attackers. Twenty-four people were seriously wounded, including an Austrian, a German and a Dutchman.
ISIL said in its claim of responsibility that “a group of soldiers of the caliphate in Indonesia targeted a gathering from the crusader alliance that fights the Islamic State in Jakarta.”
Police confirmed that ISIL was responsible and named Bahrun Naim, as the mastermind.
They believe Naim leads a network known as Katibah Nusantara and is pulling strings from Raqqa, ISIL's de facto capital in Syria.
“His vision is to unite all ISIS supporting elements in Southeast Asia, including Indonesia, Malaysia and the Philippines,” Jakarta police chief Karnavian said.
Fighters from those three countries have a record of working together, and several Malaysians are known to have carried out suicide attacks in the Middle East.
Indonesia has seen attacks before, but a coordinated assault by a team of suicide bombers and gunmen is unprecedented and has echoes of the siege in Mumbai seven years ago and in Paris last November.
In a recent blog post, entitled “Lessons from the Paris Attacks,” Naim had urged his Indonesian audience to study the planning, targeting, timing, coordination, security and courage of the perpetrators of the massacre in the French capital.
The country had been on edge for weeks over the threat posed by ISIL and similar groups, and counter-terrorism police had rounded up about 20 people with suspected links to ISIL.
There was a spate of attacks in Indonesia in the 2000s, the deadliest of which was a nightclub bombing on Bali that killed 202 people, most of them tourists.
Police have been largely successful in destroying domestic insurgent cells since then, but officials have more recently been worrying about a resurgence inspired by ISIL.
Al Jazeera and Reuters