Prime Minister Benjamin Netanyahu said the Iran-backed Huthis will pay a "heavy price" for the attack, which started a fire and caused some damage near Tel Aviv, Israel's commercial hub.
Palestinian resistance movement Hamas, whose October 7 attack triggered the war, praised the missile launch, vowing that Israel "will not enjoy security unless it ceases its brutal aggression against our people in the Gaza Strip".
Israeli medics said several people were slightly injured while "on their way to shelters" as sirens sounded.
Glass was broken at a train station in Modiin, about 20 kilometres southeast of Tel Aviv, and police said a fragment of an air-defence interceptor had come down.
In July, a Houthi drone strike penetrated Israel's intricate air defences and killed a civilian in Tel Aviv, at least 1,800 kilometres from Yemen.
Houthi leader Abdul Malik al-Huthi said Sunday's attack was carried out with a "ballistic missile" that "penetrated" Israel's defences.
Israel said an initial inquiry indicated the missile probably fragmented in mid-air, with a military official later telling AFP it was the result of an interception attempt and the missile "was not destroyed".
Since November the Houthis have targeted Israel and its perceived interests in stated solidarity with Palestinians in Gaza, launching dozens of missile and drone strikes that have disrupted global shipping through vital waterways off Yemen.
In a televised speech on the occasion of the birthday of Islam's Prophet Mohammed, the Houthis' leader said the rebels and their regional allies were "preparing to do even more."
"Our operations will continue as long as the aggression and siege on Gaza continue," he said.
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