The fire was reported at 2:15 p.m. at the store, located at 100 Vintage Way, district spokeswoman Sandy Wargo said.
Employees at the Novato Toyota dealership across the street saw a black column of smoke coming from the roof of the building and called 911, Wargo said.
Firefighters arrived on scene minutes later and called in a second alarm because the store was in a strip mall.
"We made sure we used all our resources so it didn't spread to other stores," she said.
The fire was discovered on the roof and was controlled by 2:41 p.m., according to Wargo.
The blaze was contained to the exterior of the building on the roof. Store employees and shoppers were evacuated, and no injuries were reported during the incident, Wargo said. The sprinkler and alarm systems were not activated in the store, she said.
The fire apparently originated on a part of the roof where some electrical cords were under a fiberglass cover, Wargo said. She said investigators have not determined a cause, and that a damage estimate was not available as of 3:45 p.m.
Wargo said the blaze served as a reminder for local residents to check their electrical cords to make sure they are not overloaded, frayed or cracked.