Jose Quilabaqui, 40, and Carlos Quizhpi, 53, were ordered held in lieu of $90,000 bail after a court hearing Thursday. They've been charged with felony kidnapping.
Police Department spokeswoman Janel Sedevic said their motive was to punish the boy for misbehaving.
"The victim was struck with a belt to various parts of his body and he was subjected to buckets of ice water being poured over his body and being bathed with a garden hose," Sedevic said.
Prosecutors said Quilabaqui is the boy's father and Quizhpi is the boy's godfather.
A cousin of the teen, Diana Bermeo, defended the men, saying the boy had become involved in gang activity and that they were trying to protect him and keep him off the streets.
"It started out with him being gang-affiliated and then the drugs and stuff," she told WMAQ-TV. "My uncle, to protect him, he did what he could and to prevent him from going out at night and avoid him dying out in the street."
The teen escaped from the basement in the northwest side Albany Park neighborhood on Monday, a week after he was confined there, and contacted police, Sedevic said. He was hospitalized and released.
It was not immediately clear if the pair have attorneys. Their next court date is July 2.