The deaths of the boys, 15 and 17, saw massive protests in the Valley.
The army had initially said the soldiers made a "mistake" when they fired at the Maruti car; they were watching out for terrorists traveling in a white car. All five in the car were teenagers returning from a Muharram procession.
The Army's Rashtriya Rifles unit posted there claimed that they fired at the car when it didn't stop despite being signaled. Two died instantly, two were injured and one boy escaped to the fields.
A state government report said the car had skidded while overtaking another vehicle and hit an electric pole.
The families of the boys alleged that the firing started without warning or provocation.
Sources say the seniormost commanding officer in Jammu and Kashmir had been asked by the political establishment in Delhi to visit the families of the two boys, apologise and offer compensation.
Earlier this month, the army convicted five of its soldiers, including two officers, and sentenced them to life in jail for a staged shootout in Machhil in 2010.
Demands for ending a controversial act that gives the army sweeping powers in conflict zones have been high on the agenda of political parties in Jammu and Kashmir. The army's rulings in two major cases in quick succession are seen to be its counter-point to that demand.
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