There were large Eid prayer congregations at Eidgah, Hazratbal, Polo Ground and other places in the summer capital Srinagar.
Similar assemblies were seen in Baramulla, Sopore, Ganderbal, Bandipora, Pulwama, Shopian, Kulgam, Anantnag and Shopian towns in the Kashmir Valley.
Chief Minister Mehbooba Mufti and former Chief Minister Omar Abdullah joined the devotees for the Eid prayers at Hazratbal Shrine on the banks of the Dal Lake in Srinagar.
The biggest gathering in Jammu was at the Eidgah ground in Residency Road area where a good number of Hindus greeted the Muslims after the prayers.
Reports of large Eid congregations have also come in from Rajouri, Poonch and Doda towns of Jammu region.
While Eid prayers passed off peacefully in the Jammu region, clashes between police and stone-pelting youths occurred in the south Kashmir town of Anantnag and at Eidgah and Hyderpora areas of Srinagar.
As a precaution, authorities on Wednesday placed separatist leaders including Syed Ali Geelani, Mirwaiz Umer Farooq and Muhammad Yasin Malik under house arrest in Srinagar.
Geelani had called for peaceful protests after the Eid prayers.