Sheik Abdel-Azeem Salhab, who sits on the religious council appointed by Jordan to oversee the Islamic sites at the compound, personally reopened the gate leading into the Bab al-Rahmeh mosque on Friday, and hundreds of Muslims went inside to pray for the first time in years.
It followed days of tension between Israeli police and the Muslim religious authorities over access to a corner of the 35-acre sacred compound known to Jews as Temple Mount and to Muslims as The Noble Sanctuary.
In the build up to Friday prayers police arrested 60 people they suspected would incite violence, and boosted the security presence in the Old City. But the day passed without serious incident.
Police spokesman Micky Rosenfeld told Reuters Salhab and another person were arrested on Sunday morning, two days after the incident, for breaching an order, and that they were being held for questioning.
Salhab's lawyer said that Israeli police had banned him from accessing the compound for a week, but there was no immediate comment from the police on whether they had issued such an order.