Demonstrators seek Merkel's support for democratic forces in Iran and to join US sanctions against Iran's regime.
The Jerusalem Islamic Waqf said that 1,200 Palestinians total, managed to attend Friday prayers at Al-Aqsa throughout the day.
This Friday, September 18, Imams have been instructed to condemn the peace deals, and to warn that they pose a danger to those who signed them.
Authorities have launched an investigation into the incident.
A local resident filmed the scene as the song Mosh Khayfa by Lebanese pop star Nawal El Zoghi was played from the mosque's loudspeakers, usually used for the call to prayer.
"He said if necessary, he could psychologically analyze himself."
Gunman Brenton Tarrant, a 29-year-old Australian, is scheduled to be sentenced this week after pleading guilty to 51 murders, 40 attempted murders and one charge of committing a terrorist act.
A church was first built at the site in the 4th century, but most of the existing building dates to an 11th century church that was partly rebuilt 200 years later following an earthquake.
The mediaeval Church of the Holy Saviour in Chora, built near the ancient city walls of Constantinople, contains 14th century Byzantine mosaics showing biblical scenes.