Qaiser Sofi from Eidgah area of the city died at a hospital this morning.
After his burial, some youth indulged in stone pelting on security forces, prompting use of force by the law enforcing agencies, a police official said.
He said 12 people were injured out of which six have sustained pellet injuries.
Sofi was reported missing on October 25 and found in an unconscious state in Shalimar area of the city six days later and hospitalised, the official said.
However, local residents of the area alleged that the teen was force fed some poisonous substance by security forces.
Normal life elsewhere in the valley remained affected for the 120th consecutive day due to the separatist-sponsored strike.
While most of the shops, business establishments and fuel stations across Kashmir were shut, some were open in few areas in Civil Lines and outskirts of the summer capital Srinagar, the official said.
He said most of the public transport continued to remain off the roads but auto-rickshaws and cabs were seen plying at some places in the Valley, including in few areas of the city.
The separatists, who are spearheading the ongoing agitation in Kashmir, have been issuing weekly protest calendars since Hizbul militant Burhan Wani's killing in an encounter with security forces on July 8. The separatists have extended the strike till November 10.
While there were no curbs on the movement of people anywhere in Kashmir, restrictions on the assembly of people under Section 144 CrPC were in place throughout the Valley, the official said.
He said security forces have been deployed in strength at vulnerable spots and along the main roads as a precautionary measure to maintain law and order as well as to instill a sense of security among the people to carry out their day-to-day activities without fear.
As many as 85 people, including two cops, have been killed and several thousand others injured in the ongoing unrest in the Valley.
Around 5000 security forces personnel have also been injured in the clashes.