The Israeli military said it failed to intercept the missile, forcing many residents to leave their homes in the early hours.
The Huthis claimed responsibility for the attack, saying it used a ballistic missile directed at "a military target of the Israeli enemy".
The rebels have repeatedly launched missiles against Israel in solidarity with the Palestinians since the war in Gaza began more than a year ago. Most of them have been intercepted.
In response, Israel has struck multiple targets in rebel-held areas of Yemen, including ports and energy facilities.
"Following the sirens that sounded a short while ago in central Israel, one projectile launched from Yemen was identified and unsuccessful interception attempts were made," the Israeli military said on its Telegram channel.
In a later statement, the military called the missile strike "yet another clear example of Israeli civilians being deliberately targeted".
It stressed the country's "aerial defence is not hermetic" so Israelis should follow security instructions.
Israel's emergency medical service, Magen David Adom (MDA), said 16 people were slightly injured.
"I was at home and heard a loud explosion. I immediately went to the scene and saw significant blast damage to nearby buildings," medic Yosef Kourdi was quoted as saying in a statement released by MDA.
"MDA teams provided medical care to 16 individuals who were mildly injured by glass shards from shattered windows in nearby buildings due to the impact of the strike," the statement said.
- 'Very lucky' -
Ido Barnea, an IT manager whose apartment was damaged, told AFP a missile alert had sounded just before 4:00 am.
"Then there was a big ball of fire in the sky," he said. "I didn't even manage to get up and get dressed to go out."
An AFP photographer reported that many residents in the vicinity of the strike had to leave their homes, carrying only the essentials.
AFP images showed a large crater where the missile hit, and debris in the bedroom of a nearby house that was damaged.
Police swiftly cordoned off the neighbourhood.
Noa Mosseri, whose apartment was also damaged, told AFP she too heard the missile alert.
"We were very lucky because we didn't have time to get to a safe place. Within seconds there was a boom. We managed to get out and so we were not hurt," she said.
In their statement on Saturday, the Huthi rebels pledged to continue their attacks against Israel "until the aggression stops and the siege on the Gaza Strip is lifted".
The strike came just two days after the rebels fired a missile that damaged an Israeli school.
The military said that missile had been intercepted but only partially, and its warhead "exploded and damaged the school".
In response, Israel struck several Huthi targets in Yemen, including in Sanaa -- the first such strike on the rebel-held capital.
Rebel leader Abdul Malik al-Huthi said nine civilians were killed in the strikes.
- Warning -
Hours after the Huthi attack on Saturday, the Israeli military said it had intercepted a drone over southern Israel, which had approached from the east.
It did not specify the origin of the drone, but similar attacks have been claimed by the Islamic Resistance in Iraq group, also pro-Iran, since the Gaza war broke out.
Soon after retaliating for Thursday's attack by the Huthis, Israeli Prime Minister Benjamin Netanyahu warned the rebels of severe repercussions if there was any repetition.
"After Hamas, Hezbollah, and the Assad regime in Syria, the Huthis are almost the last remaining arm of Iran's axis of evil," Netanyahu said.
"The Huthis are learning and will learn the hard way, that those who strike Israel will pay a very heavy price for it."
On December 9, a drone claimed by the Huthis exploded on the top floor of a residential building in the central Israel city of Yavne, causing no casualties.
And in July, a Huthi drone attack on Tel Aviv killed an Israeli civilian, prompting retaliatory strikes on the rebel-held port of Hodeida.
The Huthis have also repeatedly targeted merchant vessels in the Red Sea and the Gulf of Aden that they say are Israeli-linked, prompting retaliatory strikes on Huthi targets by the United States and Britain.
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