The country's anti-terrorism office raised its threat assessment and "recommends avoiding visits to Turkey", it said in a statement.
"Yesterday's deadly attack in Istanbul, in which a group of Israeli tourists was hit, underscores the threat against tourist targets throughout Turkey."
Tens of thousands of Israelis visit nearby Turkey each year despite strained diplomatic relations between the two countries.
Besides the three killed, another 10 Israelis were wounded, foreign ministry spokesman Emmanuel Nahshon said.
Five lightly wounded Israelis were flown home overnight, medics said today.
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The three Israelis killed were identified as Avraham Goldman, 69, Jonathan Shor, 40, and Simha Damari, 60.
They were part of a group of Israeli tourists on a culinary-themed trip to Turkey, Israeli media reported.
Saturday's blast in the heart of Istanbul also killed an Iranian.
Turkey said the attack was linked to the Islamic State jihadist group.