The 17-year-old girls were reportedly acting suspiciously at the Herald Square store.
Police were called once store employees detained them and made the discovery, said Sgt. Lee Jones.
According to Jones, while initial reports indicate the remains are a fetus, the medical examiner's office is investigating.
One of the teens was taken to Bellevue Hospital to be evaluated, according to Jones, and the other is in police custody at a nearby precinct.
Both teens were charged as adults and face charges of petit larceny and criminal possession of stolen property, according to the NYPD.
The department identified them as Tiana Rodriguez, of Brooklyn, and Francis Estevez, of Queens.
Robin Hoffman, a spokeswoman for Limited Brands, which owns Victoria's Secret, said the company would have no comment because of the ongoing police investigation.