The tragic discovery was made Friday evening after crews focused their efforts further down the river. Passaic Mayor Hector Lora said the operation had turned into a recovery mission.
Emergency crews spent days searching the river using boats, helicopters, divers and sonar equipment.
The girl was with a 10-year-old boy whose body was recovered Wednesday night. Officials said the boy helped save his 11-year-old sister, who managed to get out of the water on her own and is recovering with family.
Investigators believe the three children, who are from Garfield, were playing near a boat ramp along the riverbank when they entered the water.
A man nearby jumped into the river in an attempt to rescue them, but officials said the current was too strong and the water was unusually high following heavy rainfall earlier in the week, preventing him from reaching the children.
Mayor Lora said crews expanded the search area to Newark Bay.
"You're going to see less boats in the river; this is not because we're suspending the operation, but we are now, utilizing what are referred to as cadaver dogs," Lora said. "They are able to travel over the river and pick up the scent of any body that is in the water after a certain period of time."
Garfield officials also joined the effort.
"No matter what political affiliation, no matter what county, we're all going to come together and put all our resources together to try to find this young lady," said Garfield Mayor Everett Garnto. "The water may look calm on the surface, but underneath the undertow is something that nobody sees, but it's very, very dangerous."
The principal of Garfield Middle School said the school already teaches water safety and will step up those efforts.