Khaddafy Janjalani was the country’s most wanted man with a $5m bounty on his head.
Burnham and his wife Gracia had been celebrating their 18th wedding anniversary at a resort of the island of Palawan when they were kidnapped.
Gracia Burnham was a key witness in the trial, which opened in 2003 and lasted for more than three years.
She told the court she learned from the group’s leader, Abu Sabaya, that the kidnappers had received a ransom from an unknown source, but that they still refused to free her and her husband.
|US missionary Martin Burnham was among four
killed during a rescue attempt in 2002 [EPA]
Four other rebels held in connection with the kidnapping were killed in a botched prison break in 2005.
In total, 18 defendants including one woman were brought to trial over the case, although four were acquitted in Thursday’s court ruling.
Of the four acquitted, three will remain in jail because they face other kidnapping charges.
“We are satisfied with the judgment,” state prosecutor Peter Medalle told reporters after the verdict.
The kidnapping is widely seen as having been the main trigger for the US to start providing aid and training to Philippine troops to mount offensives against the Abu Sayyaf.
The group, which is fighting for a separate Muslim state in the southern islands of the Philippines, is believed by Philippine and Western intelligence agencies to have links with al-Qaeda.
In 2000, Abu Sayyaf gunmen seized 21 European and Asian tourists from the Malaysian resort island of Sipadan. All of them were freed after Libya offered funds for their release.