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 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.
"So like, he opened the back door, set him down," said Wendell Cooper, who owns the barbershop next to the Sunset Shopping Center's parking lot.
Surveillance video showing man pulling out of parking lot after leaving baby behind. Suspect Daniel Mitchell holding newborn 2 weeks ago. pic.twitter.com/WiI5mN9SDU— Laura Anthony (@LauraAnthony7) July 25, 2017
Cooper and one of his employees were the first to spot the baby.
"I'm a father myself. I mean, it just bothers me," said barber Erick Keeton. "Like I said, I initially found the baby, I brought him in, made sure he was fine. Checked him out, he seemed cool. So it was a little confusing as to why he would leave his kid."
Mitchell was arrested a short time after the baby was abandoned in an unrelated hit-and-run.
"It's pretty shocking. The officers that responded were surprised to learn that the baby was left in a parking stall," said Sgt. Jose Martinez.
Ta Gred was inside the barbershop when paramedics were treating the baby.
"I was like, 'This guy must've been crazy or intoxicated,' just like leaving a baby in the lot like that. I was more shocked than anything," she said.
"We brought it inside, and we waited 10 minutes because we thought they would come back, that they forgot the baby," Cooper said. "And then we went next door and watched the video and seen the guy pull up and set him on the ground."
Cooper has pictures of the baby on his phone. He said he plans to keep them, saying maybe the boy will come back one day and he can show him the photos.
"I'll keep that one, I'll keep it. I might meet him when he gets a little older. He will need a haircut -- he had a lot of hair to be 16 days old, a lot of hair. Hopefully we will meet him when he is 1, 2 years old," said Cooper.
California law states that you can leave a baby at a safe surrender spot such as a fire station.
The fire chief of Suisun City said he would have been happy to care for the little boy.