Police said the Dodge Caravan, located late Friday afternoon, was a rental vehicle and was returned to the rental car company.
Authorities are not disclosing the location of the van, because they want to search for additional evidence.
In the meantime, the boys' mother pleaded for their safe return.
Azucena Quinones is desperate to find her children, 2-year-old Justin and 4-year-old Jacob, who were abducted on Thursday night outside of her apartment in Anaheim.
"All I want from you is to bring my children back and safe. I'm not going to put nothing over you. I just want my children back," said Quinones.
The brothers are believed to have been taken by their biological father and grandfather, according to Anaheim police Sgt. Bob Dunn.
Authorities said Abraham Fernandez, 23, and Louis Mendoza Fernandez, 52, live together in Houston, Texas.
"Even though it's family members that are involved, we still don't know what the motive is or how safe the kids are," said Sgt. Rick Martinez of the Anaheim Police Department.
Police said the boys and their mother were outside of their residence on the 3200 block of W. Orange Avenue taking out the trash just before 8 p.m. when a van pulled up, and two men jumped out and grabbed the young boys.
The van sped off westbound on Orange Avenue.
"We don't know what led up to this thing. We do know the woman had been in a relationship with the father of the children for seven years. They had been living in Texas," said Martinez.
Quinones said she and her children moved to Anaheim three months ago. Police said the parents were not married, and it's not clear who has custody of the kids.
An Amber Alert was issued, stretching from Southern California to Texas.
Justin is 2 feet, 6 inches tall and weighs 38 pounds. Jacob is 3 feet tall and weighs 62 pounds. Both boys have brown hair.
Justin was last seen wearing a "Buzz Lightyear" T-shirt, beige shorts and a blue jacket. Jacob was last seen also wearing a "Buzz Lightyear" T-shirt, beige shorts and a gray jacket.
Anyone with information is urged to call the Anaheim Police Department at (714) 765-1900.
The Associated Press contributed to this report.