The attacks killed 224 people including 12 Americans.Ahmed Ghailani was found guilty only in conspiring to attack the US embassies and was cleared of nearly a dozen other charges Wednesday, for which US prosecutors had hoped to put him in prison for the rest of his life.
The verdict was reached more than a week after a 12-member jury was ordered by Judge Lewis Kaplan to go into deliberations in a federal court in Lower Manhattan.
It was the first civilian trial of a Guantanamo detainee, which the Obama administration had hoped would be a test case for other terrorist cases. Military tribunals are the alternative for trying Guantanamo cases, but are slow-moving and fraught with controversy.
During the month-long trial that began in October, US prosecutors accused Ghailani of plotting and helping to organise the attacks on the US embassies.
But Ghailaini's lawyers said the Tanzanian was duped by Al Qaeda terrorist agents at work in eastern Africa with the intention of killing Americans. A key witness to Ghailani's confession of guilt was banned by the judge because Ghailani was tortured while under detention in CIA-run camps overseas.
Four other plotters in the 1998 twin embassy bombings are serving life sentences in a US maximum security prison, without parole, since their conviction in 2001 for their involvement in the attacks.
The Nairobi and Dar-es-Salaam attacks brought Al Qaeda leader Osama bin Laden to the attention of US security officials as a major mover on the terrorist scene. They bore the Al Qaeda trademark of simultaneous attacks used even more lethally in the 2001 attacks on the US.
Along with his deputy Ayman al Zawahiri, bin Laden is also listed in the US court indictments for the attacks.
Ghailani was arrested in Pakistan in 2004 and spent years in CIA-run camps, where he was alleged to have been tortured, before he was transferred to the US Naval Station's detention centre in Guantanamo Bay on Cuba.
He was moved from Guantanamo to New York last year to await trial.