Israel on Wednesday started deporting some of the 200 Turkish activists arrested during the dawn raid on the Gaza-bound aid convoy.
The captain of the largest ship arrived back at Istanbul airport to a media scrum.
The press in Turkey has reacted angrily to the incident in which four of Turkish nationals died.
The Vatan newspaper carried a front page headline that warned: ‘Nobody Should Test our Patience’.
Meanwhile, the Milliyet daily stressed that “there will be a price” for Israel to pay for the killings.
On the streets of Turkey’s largest city, residents welcomed the news that their fellow countrymen were returning home.
“The Turkish nation is overjoyed by Israel’s decision,” one man said.
“I would like to congratulate them for doing the right thing, although they are a little late to do it but they have given the right decision,” he added.
Ankara once enjoyed close ties with Israel but has now recalled its ambassador to the country.
It is the latest breakdown in relations between the two nations.
The Turkish government angered Israel in December 2008 with its outspoken criticism of the bombing of the Gaza Strip.