Yemen’s Houthi rebels launched a rare suicide attack on a Saudi frigate in the Red Sea on Monday, killing two crew members and leaving three others wounded, according to the Saudi Arabia-led military coalition fighting against them.

The Houthis, who practice an offshoot of Shiite Islam, have been fighting a war since 2015 against the coalition led by Saudi Arabia, the region’s leading Sunni Muslim power and a close U.S. ally. The rebels are supported politically by Shiite-majority Iran, Riyadh’s regional power rival, though Tehran has denied sending them weapons.

Three Houthi suicide boats attacked the frigate as it patrolled off the Hodeida port on Yemen’s western coast, the coalition said in a statement. The Houthis don’t commonly deploy suicide attackers in the battle against the Saudis and their allies. One Houthi boat hit the frigate’s tail, causing an explosion and ensuing fire, the coalition said. Saudi air force units took on the other two boats before they could strike, it said.

The frigate continued operating after the fire was extinguished, it added.

The Houthis’ official Saba news agency gave a different version of events, describing a guided missile hitting the vessel, which it claimed was carrying 176 soldiers and a helicopter.

Unverified footage shown on the Houthi-owned Al Masirah television station showed an explosion hitting a gray military boat. A plume of smoke rose from the vessel.

The Houthis have fired at ships off the Yemeni coast before, including in early October, when the rebels fired missiles twice at the USS Mason, an American destroyer. The U.S. responded by striking Houthi radar sites along the coast.

“Houthi militias’ use of Hodeida port as a base to launch terrorist attacks is a serious development that could affect international maritime navigation and the delivery of humanitarian and medical aid to the port and Yemeni citizens,” the coalition said.

Write to Ahmed Al Omran at Ahmed.AlOmran@wsj.com and Asa Fitch at asa.fitch@wsj.com