Communal tension broke out in Jalori Gate area here, which led to stone pelting, leaving at least four policemen injured in the early hours of Tuesday.
The police lobbed tear gas shells to control the situation hours before Eid in the hometown of Chief Minister Ashok Gehlot, who appealed to the people to maintain peace.
Internet has been suspended in Jodhpur to stop people from spreading rumours, and the namaz for Eid was offered under police protection, NDTV reported.
The two sides clashed with each other over installing a religious flag in connection with Eid, police said.
"Four policemen were injured in the stone pelting. Heavy police force was deployed in the area to control the situation," a source in the police control room said.
The chief minister asked the people to uphold brotherhood and called the incident unfortunate.
"While respecting the tradition of love and brotherhood of Jodhpur, Marwar, I make a touching appeal to all the parties to maintain peace and cooperate in restoring law and order," he said in a tweet.
Gehlot said he has instructed the administration to maintain peace and order.