The Pueblo girl was reported missing Thursday night after she didn't return home from school.
The suspect, Jose Garcia, 29, is also a suspect in an alleged molestation involving a different girl, Pueblo police Capt. Eric Bravo said.
The car of the man accused of kidnapping the girl broke down Friday morning in Colorado Springs, and a passerby gave them a ride to a Circle K, police said.
The girl ran into the store and asked to use the phone to call her uncle but instead called 911, which prompted the man to take off, authorities said.
Efren Vialpando told The Gazette he saw the girl come in the Circle K with two black eyes and a bruise on her lip and face. She had refused to leave the store with the man, saying, "I ain't going nowhere. I'm waiting for my momma." He said the suspect fled after that.
A Circle K employee declined to comment, citing store policy.
The girl was taken to a hospital Friday morning. Police spokeswoman Barbara Miller said details of the girl's condition won't be released because of her age.
Garcia was in custody Friday afternoon. Police haven't said how they connected him to the kidnapping or what charges he may be facing. The FBI helped with the investigation.
Pueblo County court records said Garcia was wanted for suspicion of kidnapping and sex assault on a child, though Bravo said allegations in that case involved Garcia's 9-year-old former stepdaughter. Both the former stepdaughter and the 9-year-old girl who escaped Friday attended Columbian Elementary School in Pueblo.
In the case involving the ex-stepdaughter, Bravo said Garcia was listed as an emergency contact at the school and told officials there he was picking the girl up for a dentist's appointment. Bravo said Garcia is suspected of kidnapping and sexually assaulting the girl in about a half hour before he took the girl back to school.
"We don't know if there's a connection to that girl and (the girl who escaped Friday)," Bravo said.
A family member told The Associated Press by phone that Garcia worked construction in Colorado Springs and he had known his ex-stepdaughter since she was about 3 years old.