Officials said the boy had cerebral palsy and weighed about 35-40 pounds.
Authorities tell us Jonathan's father, Jeffrey Singer, 45, drove the SUV from their home in Pasadena to his father's home on Southwick.
Police went to the grandfather's home around 4am Sunday after Singer made a statement that prompted his father to make a 911 call.
"I understand that the father of the child made some comments to his father about him being responsible for the death of the child," said Bud Corbett with the Pasadena Police Department.
Police searched the SUV and found a box with a foul odor in the back. Investigators eventually opened the box to find the body.
"It would suggest that it's probably been several days since it occurred," Corbett said.
The Harris County Institute of Forensic Science will conduct an autopsy to determine the cause of death.
Investigators were also looking for the boy's teenage sister Sunday, who was presumed to be missing. They found her alive and well Sunday afternoon and will be questioning her to see if she knows what may have happened to her little brother.
Singer was charged Sunday night with felony injury to a child by omission.
The boy's mother was arrested on outstanding warrants. She was taken away in handcuffs Sunday afternoon as police pulled evidence from their home, including a large mattress.
A fire destroyed the family's house two years ago, which is when they moved to their apartment. Those who lived near them at their house and recent apartment say they kept to themselves, but this turn of events leaves them speechless.
"It's a real shame, it's a tragedy and I'm very sorry it had to happen. God bless the kid and hopefully he is in a better place," neighbor Tony Martello said.
Neighbors told Eyewitness News Singer is a hospital maintenance worker with cancer, Jonathan had cerebral palsy and was blind and on a breathing machine, his mother was without a job and there are two other daughters in the family.
"Their house burning down, having to be forced to live in an apartment for how many months," neighbor Eric Malroy said. "I sympathize with the folks and really pray for them."
Singer's attorney said he is confident evidence will support that his client did nothing criminal to lead to the death of his son. He also said there has been no admission or confession on his client's part that he was actually responsible for the death.