The strike came a day after a Jordanian judge was shot and killed by an Israeli soldier on the Allenby Bridge, the New York Times reported. The bridge connects Jordan and the West Bank.
Israeli officials said the three Palestinians who died Tuesday had fired a mortar at its military forces. A few hours earlier, an Israeli drone crashed in the same area.
Protesters in Jordan Monday called for the expulsion of the Israeli ambassador and an end to the 1994 peace treaty with Israel.
On Tuesday, Israeli Prime Minister Binyamin Netanyahu apologized for the judge's death and said Israel was cooperating with Jordan in an investigation. He extended Israel's "sympathy to the people and government of Jordan."
"In light of our commitment to the peace treaty, Israel has already shared with Jordan the results of its preliminary investigation," Netanyahu said a statement.