Ambassador Eitan Na'eh was seen in Istanbul's main worldwide airport en route to Tel Aviv.
Turkey's Foreign Ministry says the country has asked Israel's consul general in Istanbul to temporarily leave amid an expanding diplomatic spat.
The manner of Naeh's departure angered the Israeli government, with the ambassador filmed going through an extra security check and then sitting alone at the gate.
In a statement issued by the Israeli Foreign Ministry, Gürcan Türkoğlu was summoned and asked to return to his country, considering the latest development on bilateral relations between Jerusalem and Ankara.
"The [central bank] is closely monitoring the unhealthy price formations in the markets", the bank said in a statement.
President Tayyip Erdogan described Monday's bloodshed, the deadliest for Palestinians since the 2014 Gaza conflict, as genocide and called Israel a terrorist state.
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Turkey told Israel's ambassador to leave the country after Israeli forces killed 60 Palestinians during protests on the Gaza border against the opening of the US Embassy in Jerusalem.
Ankara reacted with fury to the clashes, which came on the same day the United States formally moved its embassy in Israel from Tel Aviv to Jerusalem in defiance of global criticism.
Furthermore, the Organization of Islamic Cooperation (OIC) will hold an emergency meeting in Istanbul regarding Palestine on May 18. But earlier, Erdogan spoke by telephone to Jordans King Abdullah and Malaysias 92-year-old new leader Mahathir Mohamed.
Turkey's Prime Minister Binali Yildirim addresses members of parliament from his ruling AK Party (AKP) as he arrives for a meeting at the Turkish parliament on April 18, 2017, in Ankara.
Speaking at a dinner on the first day of the Muslim holy month of Ramadan, Erdogan said the majority of the worldwide community had failed to react to the events in Gaza, and warned that remaining silent would mean "opening a very unsafe door". "It is a resistance movement that defends the Palestinian homeland against an occupying power", Erdogan wrote on his official Twitter account.