Ankara has been a vocal critic of the Israeli violence against Palestinians in Gaza and the opening of the US embassy in Jerusalem.
Turkish President Recep Tayyip Erdogan had accused Israel of "state terror" and "genocide" over the killings.
Turkey's consul general in Jerusalem was summoned by the Israeli Foreign Ministry on Tuesday and also asked to leave the country for an indefinite period of time, Turkey's Anadolu news agency reported.
At least 62 Palestinians were martyred and thousands more injured by Israeli forces along the Gaza border on Monday.
A large number of Palestinians has gathered to protest on the Gaza Strip's eastern border to commemorate the Nakba anniversary and protest the relocation of the U.S. embassy from Tel Aviv to Jerusalem.
Following the violent clashes, Turkey recalled its ambassador from Israel and the U.S. for consultations, South Africa also recalled its envoy from Israel.
The United Nations had called for an emergency meeting to discuss the outcome of the ongoing Gaza border protests.