Iwan Darmawan, 30, said he would appeal Tuesday's verdict, which was the latest in a series of tough sentences against those found guilty of terrorist attacks in the world's most populous Muslim nation.
"I am grateful to Allah for this punishment because it means I will die a martyr," he told reporters. "Why should I be afraid?"
Presiding Judge Roki Panjaitan said Darmawan surveyed the mission three times before the truck bombing, bought the explosives and helped persuade the bomber to carry out the attack, which killed mostly Indonesian passers-by and guards.
The judge said the attack was funded by al-Qaida chief Osama bin Laden and was carried out "to avenge the slaughter of Muslims by America and its allies in Iraq".
Australian Foreign Minister Alexander Downer welcomed the ruling, despite his country's oft-stated opposition to capital punishment, saying it demonstrated Indonesia's determination to punish those involved in the "heinous act".
Darmawan, also know as Rois, is the most senior of six people arrested in connection with the attack.
Three have already been sentenced to prison terms of three and a half to seven years, and prosecutors have asked for the death sentence for another man.
Darmawan has always denied any involvement in terrorism, and said that his trial was part of attempts by Indonesia's secular government to silence imams who have stepped up their campaign for the imposition of shariah or Islamic law.
"It is a grand scenario that all imams who make speeches must be detained and labelled as terrorists," he said.
Police have blamed the embassy attack on al-Qaida-linked
regional group Jemaah Islamiyah, which is also accused in the 2002 Bali bombings that killed 202 people, mostly foreign tourists, and a 2003 blast at Jakarta's J W Marriott hotel that killed 12.