Hugo Chavez had called on Israelis to stand up against their government
Israel says it has ordered Venezuela's diplomats to leave the country, following the decision by Venezuela to sever diplomatic relations.
Venezuela expelled the Israeli ambassador and his staff from Caracas on 6 January in protest at Israel's offensive in the Gaza Strip.
A week later, Venezuelan President Hugo Chavez broke off ties.
Israel has now given its response, setting a deadline of Friday for the Venezuelans to leave.
Israeli foreign ministry official Lior Hayat said the Venezuelan head of mission in Tel Aviv, Roland Betancourt, and two colleagues are now "persona non grata in Israel".
President Chavez has been a strong critic of the Israeli military's actions in Gaza, and has called on Israelis to stand up against their government.
Venezuela's Foreign Ministry has said Caracas plans to denounce Israel's military actions at the International Criminal Court, according to the Associated Press news agency.
Relations between Israel and Venezuela were already tense because of President Chavez's friendly relations with Iran, which backs Hamas and has called for Israel's destruction.
In an interview with Venezuelan state television channel VTV, the country's foreign minister Nicolas Maduro denied that the Venezuelan government was anti-Semitic.
Mr Maduro also denied that his government has relations with Hamas and the Lebanese militant group Hezbollah, the French news agency AFP reports.
Israel declared an end to its three-week operation in Gaza on 17 January. Hamas followed with its own suspension of hostilities a day later.
More than 1,300 Palestinians, including 400 children, have been killed since Israel began its land, sea and air operations in Gaza. Fourteen Israelis have died.