The Jakarta High Court said it upheld the death sentences handed to Achmad Hasan and Iwan Darmawan Mutho, alias Rois, for the September 2004 bombing.
The attack killed 12 Indonesians, including the suicide bomber.
"The panel of judges at the Jakarta High Court supports the decision by the South Jakarta district for Iwan Darmawan Mutho, alias Rois, of a death sentence," Appeals Court documents said.
The court also upheld the death sentence for Hasan in its decision sent to the District Court last week.
The judges said they backed the District Court's verdicts because both Rois and Hasan were "guilty of carrying out acts of terrorism" and had also "intentionally gave assistance to perpetrators of terror".
Rois was convicted in September this year after he told police that Al Qaeda leader Osama bin Laden had funded the embassy bombing.