The restriction came following a spate of attacks over a two-week period, which killed two Israelis and injured six.
"Due to the recent terror attacks, Palestinian women aged 16-30 years and men younger than 50 years of age must obtain permission to take part in the prayers in Jerusalem on the occasion of Ramadan," the statement by the Coordinator of Government Activities in the Territories Unit read.
On June 19, Israel allowed about 80,000 Palestinians into Jerusalem to perform Friday prayers at Al-Aqsa Mosque, the third-holiest site in Islamic religious culture, following the start of Ramadan.
Palestinians seek the diplomatic recognition of their independent state in the area of the West Bank, including East Jerusalem, currently partially occupied by Israel, and the Gaza Strip. The most recent 2014 peace negotiations between Israel and Palestine failed to resolve the long-standing conflict.