Earlier, Swiss and Spanish activists from the flotilla said they were subjected to inhumane conditions during their detention by Israeli forces.
Monday's expulsions brought the total number deported to 341, from 479 detained.
Israel's foreign ministry issued a statement, accompanied by photos of Thunberg at the airport, saying all participants' legal rights had been upheld and the only violence involved an activist who bit a female medic at Israel's Ketziot prison.
An Israeli foreign ministry spokesperson said Thunberg, a Swedish campaigner primarily for climate change, boarded a plane at Ramon International Airport in southern Israel.
Israel has dismissed the flotilla as a publicity stunt.
The deportees are citizens of Greece, Italy, France, Ireland, Sweden, Poland, Germany, Bulgaria, Lithuania, Austria, Luxembourg, Finland, Denmark, Slovakia, Switzerland, Norway, the United Kingdom, Serbia and the United States, the foreign ministry said.
Among nine members of the flotilla who arrived home in Switzerland, some alleged sleep deprivation, lack of water and food as well as some being beaten, kicked and locked in a cage, the group representing them said in a statement.
An Israeli foreign ministry spokesperson rejected the allegations.
Spanish activists also alleged mistreatment on their arrival in Spain late on Sunday after being deported.
"They beat us, dragged us along the ground, blindfolded us, tied our hands and feet, put us in cages and insulted us," lawyer Rafael Borrego told reporters at Madrid's airport.
Swedish activists said on Saturday that Thunberg was shoved and forced to wear an Israeli flag during her detention while others said they had clean food and water withheld and had their medication and belongings confiscated.
Israel's foreign ministry has described widespread reports of detainees being mistreated after the flotilla was intercepted as "complete lies".
A spokesperson told Reuters over the weekend that all detainees were given access to water, food, and restrooms, adding: "they were not denied access to legal counsel and all their legal rights were fully upheld".
On Sunday, the Swiss embassy in Tel Aviv visited 10 Swiss citizens and said all were "in relatively good health, given the circumstances".
Former Barcelona mayor Ada Colau, who was also on the flotilla, said there had been "mistreatment but that was nothing compared to what the Palestinian people suffer every day".
Spanish journalists Carlos de Barron and Nestor Prieto said Israeli authorities signed a statement on the deported activists' behalf claiming they had entered Israel illegally.
"They placed documents in Hebrew in front of us, denying us the right to a translator, and we did not receive consular assistance because they did not allow the (Spanish) consul to enter the port of Ashdod," Prieto said.
Consular staff have visited activists at the prison, according to statements from several countries whose citizens were detained.
