The attack took place when the Central Reserve Police Force or CRPF troops were withdrawing after a day-long law and order duty in Kokernag's Hiller area, about 85 kilometres from state capital Srinagar.
The stone throwers took advantage of the hilly terrain.
The driver of the armoured vehicle, Roop Singh, lost consciousness when a stone hit him in the head and the truck ran over the motorcycle in front, which the two CRPF jawans - Riyaz Ahmed Wani and Nissar Ahmed Wani - were riding.
The two CRPF jawans were rushed to a hospital where they were declared brought dead.
The truck had overturned after the accident, causing minor injuries to the passengers.
Reinforcements were rushed to the spot to maintain law and order, officials said.
With inputs from PTI