The prayer was held at 6:30 AM local time, Palestine Today quoted Jerusalem Islamic Waqf as saying.
Thousands of Palestinians in Gaza also marked the Eid in the morning by saying the prayer. Senior Hamas members also attended the ceremony.
Mahmoud al-Zahar, a member of Hamas Political Bureau, addressed the event, highlighting that occupation and siege will not stop the Palestinian nation from moving on the path of liberation.
The month of Ramadan ended but there is no end to the braveries of the Palestinian people and the love for al-Quds, he said.
Ramadan is the ninth month of the Islamic calendar, observed by Muslims worldwide as a month of fasting, prayer, reflection and community.
At the end of Ramadan, when the month of Shawwal beings, Muslims celebrate Eid al-Fitr.