A top security official said Abd al-Wahab and Muhammad Amin were killed in an exchange of fire with Indonesian forces in the troubled province of Aceh.
Wahab was said to be GAM's district police chief, while Amin was a military commander.
They were killed after a tip-off from locals led the security forces to their hideout.
Seeking independence of Aceh from Jakarta, rebels belonging to GAM have been engaged in a bitter conflict with Indonesian forces.
Jakarta launched a renewed military offensive against the rebels months ago after peace talks between the two collapsed.
The Indonesian army claims to have killed 700 rebels and arrested 1500 others since the offensive was renewed.
But human rights activists fear that the dead may even include many civilians.
The province of Aceh in the northern tip of Sumatra island has been wrecked by violence since 1976, when the struggle for independence first erupted.
An estimated 10,000 people have died in the continuing violence so far.