The shooting occurred around 11:38 a.m. at the store on the 1600 block of East Highland Avenue. The victim, 39-year-old Nelly Kantun, was the restaurant manager.
Police believe 55-year-old Pedro Enrique Duquesne confronted the victim inside the Domino's Pizza, opened fire and continued to shoot as she tried to escape.
Kantun suffered multiple gunshot wounds to her abdomen. She was taken to St. Bernardine Medical Center, where she was pronounced dead.
Kybree Edmond, who was working as a security guard at the Walgreens next door, saw the victim run out and collapse.
"When I saw her laying there, I just went into shock a little bit. She was there gasping for air, fighting for her life," said Edmond.
Witnesses saw the suspect driving away from the scene in a black 1993 Honda Accord. Duquesne was eventually located Wednesday evening and taken into custody near Waterman Avenue and Mill Street.
Investigators said the suspect admitted to committing the crime. They said the couple had apparently been having relationship problems.
The investigation is ongoing. Anyone with information was asked to contact San Bernardino police at (909) 384-5656.