In a statement, Jerusalem's Jordan-run religious endowment authority said the dawn prayer was held on time inside the mosque after Israeli authorities closed the site for several hours.
The compound was shut down Friday evening after Israeli forces shot dead an Israeli-Arab suspected of attempting to stab a police officer at a mosque gate in Jerusalem.
Speaking to Anadolu Agency on Friday, Al Aqsa Mosque director Sheik Omar Kiswani said Israel has made the closure of the holy site a regular occurrence.
Israeli police have shut down the Al Aqsa compound twice in the past month.
For Muslims, Al-Aqsa represents the world's third-holiest site. Jews refer to the area as the "Temple Mount", claiming it was the site of two Jewish temples in ancient times.
Israel occupied East Jerusalem during the 1967 Middle East War. It annexed the city in 1980, claiming it as the capital of the self-proclaimed Jewish state in a move never recognized by the international community.
