A bus, a car and a house were also set on fire in the latest flare-up in the western Uttar Pradesh city, where a curfew was imposed after the clashes yesterday.
A government spokesperson said prohibitory orders still remain in effect, but did not say whether the curfew had been lifted.
Fire brigade personnel were deployed to douse the fires.
"In all, 49 accused persons have been arrested. Efforts are on to arrest the rest of the accused," the UP Police said.
Elaborating on the genesis of the clashes, the police said in a statement that a few people were riding motorcycles carrying the tricolour and were chanting Vante Mataram and Bharat Mata Ki Jai.
As the procession reached minority community-dominated Baddunagar, "anti-social elements" pelted stones and opened fire. "In this (firing), Chandan was killed and Naushad was injured. Naushad was referred to Aligarh for treatment," it said.
The two were undergoing treatment at Jawaharlal Nehru Medical College in Aligarh. Naushad was out of danger and Akram was being operated upon, the hospital authorities said.
The motorcycle rally was taken out by VHP and ABVP volunteers as part of celebrations on the 69th Republic Day.
Meanwhile, the police today stopped firebrand leader Sadhvi Prachi in Aligarh and prevented her from visiting Kasganj. She, however, said: "If the district administration really wanted, then it would had not allowed the violence."
Earlier today, Additional DG (Law and Order) Anand Kumar said "anti-social elements today tried to set on fire a small shop on the city's outskirts... Some of them have been taken into custody, while others were chased away."
The police was trying to make people "understand communal bonhomie", he said adding that the situation was under control now. "Sufficient police personnel have been deployed."
Superintendent of Police, Kasganj, Sunil Kumar Singh, said: "Anti-social elements had set two shoe shops on fire in Ghantaghar market, and fire brigade was pressed into action.
"Apart from this, one utensil shop was set afire and a bus was also damaged by anti-social elements, who set it on fire. Fire brigade was called in to douse the fires."
But Samajwadi Party spokesperson Sunil Singh 'Sajan' demanded more than just assurance from the state government.
"The UP government must act tough on the anti-social elements, so that this acts as a deterrent for others."
UP Congress spokesperson Virendra Madan suggested the violence was connected to Lok Sabha polls, due next year.
"The state government must show seriousness and control the situation at the earliest... Is there any possible link of this violence with 2019 Lok Sabha elections for polarisation?"
Speaking to reporters in the evening, ADG Agra, Ajay Anand, said: "As many as 39 preventive arrests have been made for violating Section 144 of the CrPC and nine persons have been arrested under sections of IPC."
The details of one more arrest was not immediately clear.
"Our preventive action is still going on. We are arresting those who are violating Section 144 of CrPC," Anand added.
Divisional commissioner of Aligarh, Subhash Chandra Sharma, said the violence erupted after the cremation of the boy, who died yesterday.
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