The incident, which was caught on surveillance video, occurred at the business located on the 24700 block of Madison Avenue around 11:47 a.m.
Police say the child was in the garden center with an adult family member while his father was shopping nearby. The Akita was with his owner on a leash near the child.
Investigators say the boy apparently went to pet the dog when the dog bit the child in the head. The father rushed to his son's aid and spoke with the dog's owner, who then apologized and left the area.
The 3-year-old was transported to Inland Valley Region Medical Center for treatment. He sustained tears to his forehead, jaw neck and around his right eye, requiring over 50 stitches.
The child was later transferred to Rady's Children Hospital in San Diego for additional treatment.
Photos from the surveillance video were circulated to a local news outlet, and the dog's owner was ultimately identified as a 62-year-old resident of Murrieta.
On Sunday, detectives contacted the owner. That's when Akita was quarantined by the Animal Friends of the Valley.
The investigation is ongoing. Anyone with information was urged to contact Detective Jeremy Durrant at (951) 461-6354.