Prosecutors asked the judge to revise the instructions he gave on what constitutes a war crime to the jurors.
Defence lawyers said the instructions were correct, but that if the judge found otherwise, a mistrial should be declared.
Hamdan faces a possible sentence of life in prison if at least four of the six-member jury find him guilty.
Even if found innocent, he might not be freed, since the US military reserves the right to indefinitely hold "enemy combatants".
Prosecutors said Hamdan was trained to use weapons at an al-Qaeda camp and also "delivered weapons, ammunition or other supplies to al-Qaeda members and associates".
|Hundreds of prisoner remain in detention
at Guantanamo Bay [GALLO/GETTY]
"Hamdan was al-Qaeda, every fact in this case points to that," said John Murphy, a US prosecutor, in closing arguments on Monday, describing Hamdan as an "al-Qaeda warrior".
"This is a classic case of guilt by association," Lieutenant Commander Brian Mizer, an assigned military defence lawyer for Hamdan, told the court.
"Mr Hamdan is not an al-Qaeda warrior, he is not al-Qaeda's last line of defence," Mizer said.
"He's not even an al-Qaeda member."
Hamdan is the first to undergo a full trial at the Guantanamo Bay prison camp and the case is an important test of the military commission system set up as part of the Bush administration's 'war on terror'.
The Yemeni was captured at a roadblock in southern Afghanistan in November 2001, allegedly with two surface-to-air missiles in his car.
He 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.
Hamdan has already spent six years in prison at the Guantanamo prison camp, and his defence lawyers say he was subjected to abuse while in US custody, including humiliating interrogation tactics and sleep deprivation.
The Bush administration has faced heated criticism over the Guantanamo Bay prison camp and the special tribunals, which operate under different rules to other civilian or military courts.
Only a small group of authorised observers and journalists are allowed into the small courtroom and military authorities prohibit the proceedings to be recorded by television news networks.