Hundreds of protesters stormed a polling station at Pakherpora in Chrar-e-Sharief area of Budgam district and ransacked the building, officials said.
Security forces fired several warning rounds to disperse the mob which did not relent.
Six persons were injured in the firing, of whom two later succumbed to injuries. Those killed were later identified as 20-year-old Mohammad Abbas and 15-year-old Faizaan Ahmad Rather, the officials said, adding both died of bullet wounds.
In another incident, security forces opened fire to quell a stone-pelting mob in Ratxuna Beerwah area, leaving one Nissar Ahmed dead.
The officials said the BSF, deployed for security of the polling stations, fired live rounds as they were not provided with pellet guns.
Violence marred polling in some other parts of the Srinagar parliamentary seat as polling staff and security force personnel were forced to abandon two polling stations in Chadoora assembly segment as they came under heavy stone- pelting by mobs, the officials said.
Stone pelting incidents were reported from over two dozen other places across the three districts of Srinagar, Budgam and Ganderbal which constitute the Srinagar constituency, the officials said.
The voter turnout has been low so far with only 3.3 per cent of the 12.61 lakh electorate exercising their franchise in the first four hours of polling, the officials said.
Even in traditionally high turnout areas like Budgam, Ichgam and Maloora, many voters chose to give polling a miss.