Officials say lightning sparked the fire at a storage tank of the Puerto La Cruz refinery, sending large plumes of black smoke into the sky and leading to the evacuation of the surrounding area.
The authorities say no one was injured.
An explosion at the country's largest refinery killed 55 people last year.
The Puerto La Cruz refinery can produce nearly 200,000 barrels of oil a day.
Production 'not affected'
Production has not been affected by Sunday's blaze, Mr Chavez said.
Soon after a storage tank was reportedly hit by lightning at 15:15 local time (19:45GMT), authorities ordered the evacuation of residents within 1km (half a mile) of the plant on the Caribbean coast as a precaution.
Large thunderstorms are currently drenching the country, says the BBC's Irene Caselli, in Caracas.
After teams on the ground fought the fire for more than two hours, President Nicolas Maduro wrote on Twitter that the fire had been "controlled".
Venezuela has the largest oil reserves in the world.
A year ago, an explosion at the country's largest refinery killed 55 people and halted production.
The Puerto La Cruz refinery is one of six PDVSA facilities operating in Venezuela.
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