The video apparently shows the rebels kicking and pushing the soldiers into a corner before opening a barrage of bullets and executing them.
The Human Rights body says the incident, if confirmed, could amount to a war crime.
“This shocking footage depicts a potential war crime in progress, and demonstrates an utter disregard for international humanitarian law by the armed group in question,” a statement from Amnesty International read in part.
No group has claimed responsibility for the actions although many suspect that Islamist group, the al-Nusra Front may have carried out this grisly crime.
This comes a day after U.S secretary of State Hillary Clinton warned the Syrian rebels to desist from extremism saying the so called revolution could be hijacked by Islamic fundamentalists.
The condemnation by Amnesty International will be a matter of concern for Western countries that have been supporting the Syrian rebels.
The crisis in Syria has left an estimated 36,000 people dead as rebels try to dislodge President Bashaar Al Assad.