According to eye witnesses, the Jews who entered the holy site were singing, while the Arabs called out "Allahu Akbar."
Police forces that arrived at the scene had to separate the warring sides and remove the Jews from the Temple Mount.
The Jerusalem Police said that several Jewish visitors broke the rules of conduct and created provocation, leading to their removal from the site.
Nevertheless, visits to the Temple Mount were allowed to continue.
This week is one of the more sensitive and explosive weeks in Israel in general and in Jerusalem in particular.
The Jerusalem District Police has bolstered its forces, bringing thousands of police and Border Police officers from other areas of the country to the capital starting Sunday ahead of Jerusalem Day celebrations, the opening of the US Embassy in the city and Nakba Day.