The car had already been found outside an apartment complex, but Genesis Haley, 8 months old, was not inside.
Hong Nguyen told KTRK-TV she decided to take a different route Monday for her morning run. When she heard the crying and discovered Genesis still strapped in her car seat, she dialed 911 and stayed with the baby.
Police said Genesis was unharmed.
"God was watching over this child even the witness who found the cild said she decided to turn left as she was jogging. For some reason, she made a left," said Jesus Sosa, a spokesman for the Houston Police Department.
The baby's mother told police she left Genesis sleeping in her car seat when she went into the convenience store at a Texaco gas station. She also left the car running and from inside the store saw a man get into her Saturn and drive off.
An Amber alert was issued. Police have since released a sketch of the suspected car thief.