Four others were sentenced on Wednesday to prison terms ranging from five to 10 years.
Jamal al-Badawi, a 35-year-old Yemeni, and Saudi-born Abd Al-Rahim al-Nashiri were both sentenced to death for plotting, preparing and involvement in the bombing.
The attack, which was blamed on Usama bin Ladin's al-Qaida network, killed 17 American sailors as their destroyer refuelled in the southern Yemeni port of Aden.
Al-Badawi, who was in the heavily guarded court to hear his sentence along with four other Yemenis charged in relation to the bombing, would appeal the sentence, his brother, Muhammad al-Badawi, said.
Al-Nashiri, believed to be the mastermind of the 12 October 2000 bombing, was the only one of the six men convicted by the judge not to be in court as he is being held in US custody at an undisclosed location.
Jamal al-Badawi, 35, has been
handed the death sentence
The US announced al-Nashiri's arrest in 2002. He was detained in the United Arab Emirates and transferred to American custody. US officials believe he is a close associate of Saudi-born Usama bin Ladin.
In addition to the Cole attack, al-Nashiri is suspected of helping direct the 1998 bombings of US embassies in Kenya and Tanzania.
The six men were all charged with belonging to al-Qaida and playing various roles in the attack on the USS Cole, which was carried out by bombers Ibrahim al-Thawr and Abd Allah al-Misawa, both Yemenis, who rammed an explosives-laden boat into the naval destroyer.
Judge Najib al-Qadiri sentenced Fahd al-Qasa to 10 years in jail for filming the bombing, which left a gaping hole in the side of the destroyer, which was later repaired and returned to service.
Fahd al-Qasa received 10 years
for filming the bombing
Maamun Masuh received an eight-year prison term for delivering money used in preparing and executing the attack and assisting al-Badawi.
Ali Muhammad Salih and Murad al-Siruri were both sentenced to five years in prison for forging identification documents for al-Misawa, one of the bombers.
All the men sentenced on Wednesday are expected to appeal their sentences within 15 days, according to al-Badawi's brother.