Thunberg, 22, was put on a flight to France on Tuesday, the ministry said, adding that she would travel on to Sweden from there.
Three other people who had been aboard the charity vessel also agreed to immediate repatriation. Eight other crew members are contesting their deportation order, said a statement from Israeli rights group Adalah that advised them.
They will be held in a detention centre ahead of a court hearing. It was not immediately clear when that would happen.
Israeli forces boarded the charity vessel as it neared Gaza early on Monday, trying to break through Israel's longstanding naval blockade, which has gained international attention since Israel also cut off land access to the strip in March. Israel now allows in only limited supplies of food distributed by a group it backs.
The British-flagged yacht was taken to the Israeli port of Ashdod and the 12-strong crew were transferred overnight to Ben Gurion airport.
The activists had been carrying a small cargo of humanitarian aid, including rice and baby formula, and said they wanted to raise international awareness about the humanitarian crisis in Gaza, which has been devastated by months of war.
Israel dismissed the voyage as a pro-Hamas publicity stunt. "The tiny amount of aid that was on the yacht and not consumed by the 'celebrities' will be transferred to Gaza through real humanitarian channels," the Foreign Ministry said.
Israel released an image of Thunberg sitting on a plane ahead of its departure for Paris. She usually refuses to fly because of the carbon emissions of the airline industry.
Organisers released a video of Thunberg on Monday, filmed on board the vessel before it was captured, in which she said that if it were taken that would mean Israel had kidnapped her and the rest of the crew in international waters.
US President Donald Trump mocked this: "I think Israel has enough problems without kidnapping Greta Thunberg," he said. "She's a young, angry person ... I think she has to go to an anger management class."
Israel has imposed a naval blockade on the coastal enclave since Hamas took control of Gaza in 2007. Israel says it aims to stop weapons from reaching Hamas.
The blockade has remained in place through conflicts including the present war, which began when Hamas-led militants rampaged through southern Israel on October 7, 2023, killing more than 1200 people and taking 251 hostages by Israeli tallies.
Israel's retaliatory offensive against Hamas has since killed more than 54,000 Palestinians, according to health officials in Hamas-run Gaza, and destroyed most of the homes of its 2.3 million residents.
In March Israel imposed a total blockade of all supplies reaching Gaza, which the United Nations says has driven the population to the brink of famine.
Over the past two weeks Israel has allowed in limited food supplies to be distributed by a new Israeli-backed group, a step Israel says is necessary to prevent Hamas from diverting aid.
