Dozens of young men pelted stones at police personnel in the towns of Baramulla, Sopore and Anantnag.
Stoning was also reported from Lal Chowk, the heart of Srinagar, as well as Hyderpora and other parts of the city's old quarters.
The administration had placed senior separatist leaders including Syed Ali Geelani, Mirwaiz Umer Farooq, Shabir Ahmad Shah and Muhammad Yasin Malik under house arrest to maintain peace.
Keeping in mind the Eid atmosphere, police exercised restraint while dispersing the protesters.
Jammu and Kashmir Chief Minister Omar Abdullah offered Eid prayers at the Hazratbal shrine in Srinagar.
Former chief minister and Peoples Democratic Party leader Mufti Muhammad Sayeed offered prayers in Sonawar area of Srinagar.
A police officer said that barring these few incidents, Eid celebrations were celebrated peacefully in the valley.
"Except for stray incidents of stone pelting at some places, Eid prayers passed off peacefully," the officer told IANS.
"Large gatherings were seen in Srinagar at Hazratbal and Eidgah grounds where hundreds gathered to offer prayers," he said.