The fire was reported around 7:40 a.m. Firefighters arrived five minutes later and saw smoke in the west side of the building on Range Avenue, Santa Rosa fire Battalion Chief Mark Basque said.
Basque said an electrical malfunction in the main electrical and utility room outside the store started the fire.
The small, smoldering fire burned some debris and plastic in the utility room, and a construction worker put out the fire with an extinguisher, Basque said.
The store is undergoing interior renovations.
Smoke traveled throughout the store through conduits containing electrical wiring and through electrical sub-panels, Basque said. It caused minor to moderate damage to the first and second floors of the three-story building, Basque said.
One of the store's doors leads to the interior of the rest of the mall on Guerneville Road. That area sustained only a light haze and no smoke damage, and remained open, Basque said.
JC Penny was the only store to lose electricity, Basque said.
Firefighters used exhaust fans to clear the smoke out of the building, Basque said.
Mike Gobble, JC Penny store manager, said the store is closed at least through today and may reopen on Friday. None of the employees who were in the store before it opened were injured, he said.
"It sounded more serious that it was," Gobble said.
The fire caused several thousand dollars in damage to the electrical panel, and JC Penny will have to determine the amount of smoke damage to its clothing and other merchandise, Basque said.
