The Dutch-flagged MV Hondius is due in Rotterdam on Sunday for disinfection. More than 25 crew members and medical staff remain aboard, along with the body of a German passenger who died during the voyage.
Spanish authorities said 125 passengers and crew from 23 countries were evacuated over two days.
“Mission accomplished,” Health Minister Mónica García Gómez said. “Between yesterday and today, we have evacuated the 125 passengers and crew members from 23 countries... The ship... left the port today at 7 p.m. (1800 GMT).”
The final group of evacuees was flown to the Netherlands on two charter flights early Tuesday.
One French passenger later tested positive and was placed in intensive care in stable condition, officials said. A Spanish case has also been confirmed, while others remain under review.
WHO chief Tedros Adhanom Ghebreyesus said the situation was contained, adding: “This is not another Covid.”
The outbreak is believed to have begun before departure from Argentina, where hantavirus is endemic, with possible onboard transmission under investigation.