The couple have been arrested and were led away in handcuffs from their home in the village of Gross Schacksdorf near the Polish border.
Police said the girl had been kept "most of the time" in a locked cupboard and suspect she was sexually abused over a "long period."
She was found in a vacant apartment next to her mum and stepdad's flat.
While the girl was in care the pair allegedly wrote a fake letter to themselves, purporting to come from her, saying: "Dear mum and dad, I ran away because I can't stand it anymore to be in the home."
Petra Hertwig of the Cottbus Public Prosecutor's office, said: "In the course of the arrests on Sunday, computers, video files and film equipment were seized, which are currently being evaluated by investigators."
Four masked officers of the elite SEK police unit – usually involved in hostage and terrorism incidents – smashed down the door of the couple's apartment to free the girl.
The teenager went missing from the Käthe-Kollwitz-Home in Cottbus in October last year.
She had been placed there by social services because of the "volatility" of her mother and stepfather.
During the police probe, police searched the family home six times, but it was only on Sunday that they entered the vacant apartment.
Prosecutors confirmed that a 52-year-old woman and a 46-year-old man are being probed for suspected sexual assault.
Both are being held in separate high security jails as the investigation continues.
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