The gun battle near the famous Mughal gardens, which started in Srinagar on Thursday night heightened tensions in the Ishbar locality and its adjacent areas.
Police said on specific information, a raiding party of the army, police and paramilitary surrounded a house in the Ishbar locality and tried to enter it when the holed up militant's hurled grenades followed by automatic gunfire.
"We have killed three militants including two Pakistanis and a local during the five hour long gun battle. Three AK-47 rifles, three magazines, one hand grenade and 130 rounds were recovered from the encounter site," a senior police officer here said.
In another nightlong gun battle in south Kashmir Panzpura village near Bejibehara in Anantnag district, one army soldier and one militant were killed.
"The operation is still continuing in Bejibehara," a police spokesman in Srinagar said.