Al Jazeera's Tom Ackerman, who is at the trial in Guantanamo Bay, said that the jury, comprised of US military officers, has since retired and is to resume deliberations on Hamdan's sentence on Thursday.
The jury had deliberated for about eight hours over three days following the two-week trial.
Hamdan, wearing a white turban and long white robe, stood tensely in the courtroom beside his lawyers as the verdict was announced, listening via headphones to the tribunal's English-Arabic interpreter.
He later wept into his hands when the guilty verdict was announced.
War crimes charge
|Hundreds of prisoners remain in captivity
at Guantanamo Bay [EPA]
The Bush administration has faced heated criticism over the Guantanamo Bay prison camp and the special tribunals, which operate under different rules to other military courts or civilian ones.
Tony Fratto, a White House spokesman, said after the verdict that the Bush administration was pleased that Hamdan had received a "fair trial".
However our correspondent says the prosecution is likely to be disappointed by the verdict.
Hamdan was captured at a roadblock in southern Afghanistan in November 2001, allegedly with two surface-to-air missiles in his car but was cleared on conspiracy to commit war crimes.
"The jury had apparently heeded the defence's contention that it cannot be a war crime to intend to use weapons against soldiers on the field of battle," Ackerman said.
The ruling on this issue could provide an important precedent for the other 80 detainees set to face military tribunals at Guantanamo.
It was the Bush administration's third attempt to try Hamdan, who won a US supreme court victory in 2006 that meant the first version of the Guantanamo court system was scrapped.
The charges against him were twice dropped and refiled.
The counts he was cleared of - two counts of conspiring with al-Qaeda to attack civilians, destroy property, commit murder in violation of the laws of war - were the only charges against him in the first prosecution attempt.
Hamdan says he drove for bin Laden in Afghanistan because he needed the $200 in monthly wages but denies joining al-Qaeda, pledging loyalty to bin Laden or participating in attacks.
His defence lawyers say he was subjected to abuse while in US custody, including humiliating interrogation tactics and sleep deprivation.
The American Civil Liberties Union said it viewed the military tribunal process as deeply flawed.
"Any verdict resulting from such a flawed system is a betrayal of American values,"
said Anthony Romero, the ACLU's executive director.
"The rules for the Guantanamo military commissions are so flawed that justice could never be served. From start to finish, this has been a monumental debacle of American justice."