The company, known also as PDVSA, said a fire broke out at the Puerto La Cruz refinery following a lightning strike. The facility can process 187,000 barrels of oil per day.
Refining Vice President Asdrubal Chavez said the fire was extinguished by Sunday evening after burning for more than three hours.
"We are prepared for this type of event," he said in a statement.
There were no injuries reported during the incident. Chavez said there was only minimal damage to the refinery. Parts of the refinery not affected by the incident continued to operate as normal, he said.
More than 40 people were killed and dozens more were injured when an explosion ignited two gas storage tanks at the Amuay refinery, the largest in Venezuela, in August 2012. The accident was one of the deadliest in the industry and forced the shutdown of a facility capable of processing 645,000 bpd.
Venezuela ranked 6th in terms of oil production for July from members of the Organization of Petroleum Exporting Countries.