The two deceased have been identified as twenty-year-old Javid Ahmad Bhat and twenty-four-year-old Suhail Javid Lone, reported the local newspaper Greater Kashmir.
Another youth was rushed to a hospital here in a critical condition for specialised treatment, they said. Like in previous tense situations, the issue of the controversial killings in the volatile border state looks set to snowball into a bigger crisis.
The deputy commissioner of Shopian has been asked to probe the incident and submit a report within 20 days.
The defence spokesman said, "An Army administration convoy was passing through Ganovpora when it came under unprovoked and intense stone-pelting by a group of 100-120 stone-pelters".
"The crowd surrounded an isolated portion of the convoy and tried to set them on fire".
The statement further added that a junior commissioned officer accompanying the convoy got hit and fell unconscious. He was seriously injured.
He claimed that the locals tried to "snatch weapons from army jawans" and they "took the preventive measure".
Two civilians were shot dead by Indian Army personnel in the restive region of Kashmir on Saturday, 27 January, triggering serious concerns in the valley.
The Jammu and Kashmirpolice on Sunday booked an Army major and his associates on charges of murder, attempt to murder and endangering life in Saturday's shooting incident in a remote village of southern Shopian district.
Vakil while condemning the killings said the blood of Kashmiris has become so cheap that it is being spilt on daily basis and without justification.
"It was a conspiracy of Pakistanis and separatists to target the army vehicles in Shopian yesterday and around 200 goons, criminals, anti-nationals targeted one of the vehicles and injured seven army jawans", Raina said.
Condemning the killing of civilians in Shopian, PDP leader, and MLC Zaffar Iqbal Manhas has said such recurrent incidents should force the powers-that-be to do some soul-searching and face the reality that Jammu & Kashmir is an issue which calls for a solution to prevent further loss of lives.