Authorities said several people were injured. Demonstrators attacked the store near the school in Gurgaon near New Delhi after riot police thwarted their attempt to storm the campus.
The boy's body was found in the Ryan International school's lavatory on Friday with his throat slit with a knife. Police said a school bus attendant, who was arrested hours after the incident, had admitted attacking the child after he resisted a sexual assault.
Angry parents had tried to storm the campus on Saturday, a day after they vandalised part of the school building to press demands for criminal charges against the school management.
"We had to use force to disperse the protesters after our warning had no effect," Gurgaon police commissioner Sandeep Khirwar told AFP.
Enraged parents scuffle with Indian police after boy killed resisting sexual assault in school
Residents told television channels the shop was targeted because several staff members had been seen previously consuming alcohol during school hours.
Parents have demanded that the school's operating licence be cancelled. Authorities have ordered it closed until further notice to avoid violence.
The incident has caused widespread anger and sparked concern over safety standards in schools.
India's swelling middle class has fuelled the growth of private schools in a country with a crumbling public education system.
On Saturday police arrested a man after he allegedly raped a five-year-old girl inside a classroom in New Delhi.
India has a grim record of sexual assaults on minors with 20,000 cases of rape or sexual assault reported in 2015, according to government data.
A UN Committee on the Rights of the Child in 2014 said one in three rape victims in India was a minor. Almost half the abusers are known to the victims.
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