Her body was found around 10:00 p.m. in a recycling container not far from her Clayton home.
Autumn was last seen alive while leaving her home on her white BMX bicycle on Saturday afternoon.
Police had been looking for that bike, which was finally found late Tuesday morning in a home next door to where her body was discovered.
Officials tell Action News that Autumn's body was still dressed in the same clothes she had on Saturday.
An autopsy will be conducted by the Gloucester County Medical Examiner's office to determine the cause of death.
At a news conference on Tuesday morning, Prosecutor Sean Dalton said there have been no arrests and there are no persons of interest.
However, he said this is now a criminal investigation.
"If they determine if there are individuals responsible for her death, they will be held accountable," Dalton said.
Autumn's uncle, Paul Spadafora, also spoke at the news conference, saying "Our little angel Autumn has reached out to the world in her own special way. She's an angel. She was an angel here on Earth, and she's an angel up in Heaven."
The discovery comes just hours after an emotional candlelight vigil was held for Autumn in her hometown.
"This is a very sad day for the Pasquale family," Dalton said earlier in the day. His office led the search with assistance from 20 municipal, state and federal agencies. "Our hearts go out to the family and to all the residents of Clayton who stood together in support of this young girl."
Autumn, who would have turned 13 on October 29th, went for a bike ride around 12:30 p.m. on Saturday. After hours of not hearing from the girl, her family reported her missing on Saturday night at around 9:30.
The last known communication was in a text message she sent around 2:30 p.m. Saturday. Officials said there was nothing alarming or unusual about it.
Two hundred law enforcement personnel had been working on the case, along with dozens of volunteers who helped in the search for the past two days.
Police say they are now conducting a criminal investigation. Since Autumn went missing, police say roughly 75 people have been interviewed, but so far investigators have not indicated if they have any suspects in mind.
Among other things, they are reviewing information on every sex offender in the South Jersey area.
The Child Abduction Response Team (CART) has been activated. They have pulled records of every registered sex offender in the area and they are looking at surveillance video from around town.
The FBI, New Jersey State Police and the Gloucester County Prosecutor's Office are among the agencies involved.
A friend, 11-year-old DeAnna Edwards-McMillen, said Autumn was at her house Friday night and they exchanged text messages on Saturday. She said she received the last one at 1:22 p.m. and didn't believe it was intended for her. She said it read, "don't be like that."
DeAnna said her friend was nice and easy to be around. "She didn't hate people," she said in a tearful interview with The Associated Press, "and people didn't hate her."
The Associated Press contributed to this report.