The 6 800-ton ship sank off the country's southwestern coast in one of its worst maritime accidents, claiming more than 300 lives, mostly high school students on an excursion.
Nine victims were left unaccounted for, and the 145-metre Sewol was raised in March to search for them.
Bones retrieved Tuesday from the third floor of the salvaged ship matched X-rays and dental records from Huh Da-Yun, the maritime ministry said in a press statement.
She is the first of the missing students from Danwon high school to be identified following the raising of the wreck, after a piece of bone recovered two weeks ago from the sea bed where the ship had been lying was confirmed as belonging to one of two missing teachers from the institution.
Seven others still unaccounted for include the other teacher, three students and three other passengers.
The Sewol sinking and botched rescue efforts dealt a crushing blow to now-ousted president Park Geun-Hye.
Investigations concluded the disaster was the result of numerous human factors, including an illegal redesign, an overloaded cargo bay and inexperienced crew.