The shelter-in-place order was lifted about 11:15 p.m. Monday, the Contra-Costa Times in Walnut Creek reported.
The action allowed residents of the communities of Richmond, North Richmond and San Pablo to open their windows and air out their homes.
Sirens had blared after the fire broke out about 6:15 p.m. to alert residents to stay indoors and block windows and doors to help prevent them from breathing tainted air. Health officials said their main concern was crude oil and diesel fumes.
At least two fires sent thick, black smoke into the sky, the San Francisco Chronicle reported Tuesday.
Chevron officials said the fire began at the refinery's No. 4 Crude Unit. An inspection crew discovered a diesel leak in a line in the unit and the leak was enlarging.
Soon after the crew evacuated the area, the diesel ignited, refinery manager Nigel Hearne said.
All employees had been accounted for and there were no fatalities, the Chronicle reported.
The Chevron Richmond Refinery is one of the largest refineries in the United States, processing up to 240,000 barrels of crude oil a day, the company's Web site said.