Police discovered Abu Hanifa and Riyazuddin Ali, both in their early 20s, both severely injured. "By the time we took them to the hospital at night they had succumbed to their injuries," police Superintendent Debaraj Upadhyay told AFP.
The police have made two arrests and are looking into the incident.
Videos were shot of the two victims being attacked by a large mob, who restrained their hands and savagely beat them. "There was a huge ruckus," Nagaon resident Abdul Jabbar told Benar News. "I stepped out of my house and saw dozens of villagers chasing two men. They eventually got hold of them and beat them mercilessly."
The incident is one of several in a string of cow-related incidents of late. Cows are sacred creatures in Hinduism and slaughtering one is illegal in many Indian states, including Assam.
There have even been "cow protection" vigilantes who have attacked those suspected of participating in cattle slaughtering. Upadhyay denied the involvement of any vigilantes in this most recent incident.
In April, a Muslim man in Rajasthan was beaten to death by a mob of 200 people after they discovered cows in his truck. It was later revealed that the man was a dairy farmer and the cows were for milking.
Rajasthan police were criticized for arresting Muslims for alleged violations of the cow permit laws, rather than targeting the vigilantes.
At least 10 other Muslim men have been murdered under accusations of slaughtering or eating cows since 2015.
Humans Rights Watch places the blame for these incidents at the feet of Prime Minister Narendra Modi and his Hindu-nationalist Bharatiya Janata Party (BJP). Modi firmly condemned these vigilante incidents in 2016.
Regarding the Nagaon incident, Assam lawmaker and BJP member RP Sharma said, "Branding people as cattle thieves and [killing] them is completely unacceptable. A detailed investigation will follow and anyone found guilty will be punished."
Assam-based Muslim organization All India United Democratic Front called for "an independent judicial inquiry into Sunday's incident. Of late, violence against Muslims in the state has increased and only an impartial probe will ensure that those guilty are punished."