Carter visited Hussein Lookout at Israel's northern border on Monday, for an assessment of the alleged threat from the Iranian-backed Hezbollah.
Israel claims that the Lebanese militia group has more than 100,000 missiles capable of hitting Israeli villages and cities.
"Hezbollah is sponsored of course by Iran, which is why the United States will continue to help Israel counter Iranian malign influence in the region," Carter told reporters after receiving a security briefing.
The Pentagon chief's visit comes at a time of a deep divide between the United States and its Middle East ally, with the Israeli government furiously opposing the recent deal on Iran's nuclear program.
Israel has claimed that the deal does nothing to stop Tehran from supporting armed groups outside Iran's borders, and that the Islamic Republic might still develop a nuclear weapon.
The 'ultimate objective'
Despite the tension, both Carter and Israeli Defense Minister Moshe Yaalon emphasized their close security ties at a later press conference in Tel Aviv.
"We greatly disagree when it comes to the agreement with Iran and fear for the future in the aftermath of its signing," said Yaalon. "Yet we discuss this issue in a fully open manner, alongside many other issues of great importance."
In turn, Carter said Israel remained "the bedrock of American strategy in the Middle East," underscoring the joint position on "the ultimate objective" when it comes to Iran curbing its nuclear program.
"We cannot let Iran have nuclear weapons. And there's no disagreement about the threats Israel sees every day from Iran's destabilizing activities, from terrorists like Hezbollah and Hamas and (the 'Islamic State' group)."
'Nuclear arms race'
The United States provides Israel with about $3 billion (2.8 billion euros) in military aid every year.
Israel is also the only country in the Middle East believed to have nuclear weapons. However, the government maintains a policy of "nuclear ambiguity" - never confirming nor denying the information.
On Monday, the UN Security Council endorsed the Iran deal, prompting fresh outrage from Israeli Prime Minister Benjamin Netanyahu. Speaking in front of parliament, Netanyahu said the agreement "brings war closer" and warned of a possible "nuclear arms race in the Middle East."
Carter has said the deal does not preclude the use of military force to stop Iran from obtaining nuclear weapons. He is due to meet with Netanyahu for talks on Tuesday.
Zarif praises diplomacy
In response to talk of military force, Iranian Foreign Minister Mohammad Javad Zarif said that "the world sees last week's agreement in Vienna as a victory of diplomacy over war and violence."
"Unfortunately there are still people who speak of the illegal and illegitimate use of violence to attain their objective based on illusions and insist on maintaining an ineffective option," he said, according to Iran's state news agency IRNA.
dj/cmk (AP, Reuters, AFP, dpa)