"In light of the evidence and statements of 42 prosecution witnesses, the case against Mohammad Bashir, and Mohammad Sohail who was tried in absentia, has been proven," Judge Feroz Mehmood Bhatti told the court. "Hereby they are sentenced to death for an act involving explosives, murder and terrorism."
The three are members of militant organisations Harkat Jihad ul Islmai and Harkat ul Mujahideen, both of which have close links with the Al Qaeda network.
The trial began in April 2003 and was located in the Karachi jail compound for security reasons.
"I am satisfied with the verdict. There was incriminating evidence against the two men and the judge took the right decision," Prosecutor Maula Baksh Bhatti said.
Eleven French naval technicians helping Pakistan assemble a submarine were killed when a suicide bomber in a car packed with around 150 kg of explosives rammed into a bus carrying the engineers at the car park of a luxury hotel in Karachi last year.
The men pleaded not guilty to the charges.
Expressing surprise over the verdict, defence lawyer M R Sayed said he will challenge it.
"The evidence, which was produced by prosecution was lacking in confidence," Sayed said. The accused have seven days to file a appeal in the high court.