The 15-year-old disappeared in March 2014. Police said she left a note in the mailbox of the family home in Saitama north of Tokyo reading: "Please do not try to look for me."
Her parents believed she was taken against her will but two years passed with no clue about her fate.
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That changed Sunday when she suddenly called home from a payphone at a Tokyo train station, said a Saitama police spokesperson.
Hours after the girl came under police protection, her alleged abductor, covered in blood, was found on a street in Shizuoka prefecture west of Tokyo, the spokesperson said.
He told police he had tried to commit suicide by slashing his neck with a knife, local reports said.
The girl, whose name has not been released, told police she was kidnapped by the man who had stopped her on the street on her way home from school, acccording to public broadcaster NHK and other media.
He enticed her into his car by saying her parents were divorcing, and forced her to write the note to them.
The 23-year-old man, identified as Kabu Terauchi, graduated from Chiba University east of Tokyo this month, having apparently attended school for two years while holding the girl in his apartment, the reports said.
After he graduated the pair moved to a Tokyo apartment. On Sunday she took advantage of his absence to escape.
Police plan to arrest Terauchi on charges of kidnapping a minor.
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