Biden said he also promised the Israeli leader that the United States would replenish Israel's Iron Dome rocket interception system.
The two sides continued to trade blows before the cease-fire, with Israeli air sirens warning of incoming Hamas rockets, and an airstrike in Gaza heard by a Reuters reporter.
UN emergency meeting
Earlier, at the U.N., Israel's ambassador said his government wanted a cease-fire "but only after significantly degrading Hamas' terror machine."
"This is not a war between Israel and the people of Gaza," Ambassador Gilad Erdan said.
"This is not a war between Israel and the Palestinians. This is a war only between Israel and Hamas. We will never apologize for defending our citizens, even if some countries here might be happy to see a greater number of dead Jews."
Palestinian Foreign Minister Riyad al-Maliki told reporters at the U.N., where he participated in a meeting on the situation, that "the carnage, the aggression, the attack, will stop. It is good that the Palestinian people, the more than 2 million of them (in Gaza), will be able to go to sleep tonight knowing that they will have a brighter tomorrow. But that's not enough, that's not enough at all."
The Palestinian foreign minister said the issues that triggered this latest round of violence — the situation for Muslims at their holy sites in Jerusalem and the evictions of Palestinian families in parts of the city — must be addressed.
The Biden administration had blocked efforts at the U.N. Security Council to issue a condemnation of the fighting and call for a truce, drawing criticism from some countries. All 15 council members must agree on such statements.