Daniel Mitchell, who is 18, broke down in sobs during a brief appearance in a Fairfield courtroom.
VIDEO: Abandoned baby found in Suisun City in critical condition
Police say Mitchell drove to a strip mall parking lot, pulled the car seat out and set it on the ground before driving away.
The boy was spotted almost immediately by the owners and employees of two businesses, and taken inside for safety until police and paramedics arrived.
VIDEO: North Bay dad accused of abandoning newborn in strip mall parking lot
Mitchell entered a not guilty plea to multiple charges, including child endangerment, child abandonment, and possession of cocaine.
The young father was seen in a Facebook photo dated July 10, smiling and holding the newborn.
The baby is being treated at a bay area hospital for an undisclosed medical condition and is in the custody of child protective services. His mother has not been charged.
Mitchell returns to court next month.