Officials said 17 foreigners were among the wounded, including eight Americans and citizens of Australia, Britain, Canada, Hong Kong, India, Italy, the Netherlands, Norway and South Korea.
Jemaah Islamiyah rose to prominence after the 2002 nightclub bombings in the beach resort of Bali that killed 202 people, most of them foreigners.
It staged attacks in Indonesia in each of the next three years: a 2003 car bombing outside the J.W. Marriott hotel, a 2004 truck bombing outside the Australian Embassy, and triple suicide bombings on Bali restaurants by attackers carrying bombs in backpacks in 2005.
After the government launched a massive anti-terrorism campaign, no major attacks had been reported since then — until Friday's explosions.
Remnants of the bombs found outside the hotels had circuits that were "identical" to those in explosive devices used in previous attacks on Bali, the national police spokesman said Sunday.
Police were also looking for connections between Friday's bombing and explosives discovered last week in the Cilacap region of Central Java, which were buried in a garden at the house of Noordin's father-in-law, who is also at large.
While the attacks rekindled old anxieties, Indonesians interviewed Sunday said they did not believe the bombings signaled a resurgence by the militants, who want to establish an Islamic state in the region.
The Islamist extremists enjoy little support among the country's largely moderate public.
The terrorists do not have the money or backing to launch another major attack soon, said Agus Triharso, 40, a motorbike taxi driver in Jakarta.
"Noordin Top and his friends have support from just a few hard-line Muslims," Triharso said. "As Muslims, we have to stop them."