The protesters, who posted a video of the attack on an ultra-nationalist website, tried to put hoods on them and chanting “Yankees go home”.
They also threw red paint and chased the sailors down a street.
The sailors returned unharmed to their ship, the USS Ross, which was docked nearby, a US military spokesman said.
US officials condemned the attack, but said it appeared to be a one-off event.
Turkish police arrested 12 people in connection with Wednesday’s incident, but later released them, local media reported.
The protesters, members of the nationalist Turkish Youth Union, were told they could still face charges of insult, injury and breaching laws on public protests, the Dogan news agency said.
Just before the assault, one of the protesters shouted in English at the sailors: “Because we define you as murderers, as killers, we want you to get out of our land.”
The protesters then started throwing objects at the sailors and grabbed hold of at least one of them, briefly pulling a white sack over his head.
Colonel Steve Warren, a Pentagon spokesman, called the attack “ugly and disturbing”.
He described the assailants as “local thugs”, saying they brought “great discredit upon the Turks and the Turkish reputation for hospitality”.
“We’re working closely with Turkish authorities to have this investigated and to get to the bottom of exactly what happened,” he said.
The Turkish foreign ministry also condemned the attack, calling it “in no way tolerable”.
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