Both sides declared a "united stand" on Tehran and signed a joint agreement pledging to prevent Iran from acquiring a nuclear weapon, officials said.
"We will make sure Israel will be able to defend itself by itself," Biden said during a press conference with Israeli Prime Minister Yair Lapid.
The United States is "prepared to use all elements of national power" to prevent Iran from obtaining nuclear weapons, according to a joint statement.
A senior Biden administration official told reporters in a conference call before the statement was released that the deal will further bolster the two nations' already close security partnership.
"This declaration is pretty significant, and it includes a commitment to never allow Iran to acquire a nuclear weapon and to address Iran's destabilizing activities, particularly threats to Israel," the official said.
An Israeli official called the document "a living testimony to the unique quality, health, scope, depth and intimacy of the US-Israel relationship," the AFP news agency reported.
"It takes a very clear and united stand against Iran, its nuclear program and its aggression across the region," the official, who asked not to be named, added.
Biden begins the day by meeting Lapid, who became head of an interim government earlier this month after the previous coalition collapsed.
Biden will later appear at a joint news conference with Lapid.
Both leaders will also attend a virtual summit with India and the United Arab Emirates, part of a grouping known as the I2U2.
Biden is also expected to meet opposition leader and former Prime Minister Benjamin Netanyahu, whose conservative Likud party is projected to win the most seats in the next elections slated for November.
Furthermore, Biden will receive Israel's top civilian honor, the presidential medal of honor, from President Isaac Herzog on Thursday.
Biden to meet Palestinian President Mahmoud Abbas
Biden will meet Palestinian President Mahmoud Abbas on Friday in the occupied West Bank, and will likely pledge US financial support to the territory.
Later on Friday, Biden will fly from Israel directly to Jeddah, Saudi Arabia, for talks with Saudi officials.
Ahead of Biden's visit, Saudi Arabia's civil aviation authority said it was lifting restrictions on all "all carriers" using its airspace, a possible goodwill gesture towards Israel. Biden praised the Saudi move, according to the White House.
While in Saudi Arabia, Biden will also attend a summit of Gulf allies.