Two tanks are still alight but state oil company officials say they have the situation under control.
Forty-one people died and more than 80 were injured in the blast at the Amuay refinery in northern Falcon state, one of the largest in the world.
Mining Minister Rafael Ramirez said operations could resume within two days of the site being declared safe.
A doctor at Coromoto Hospital said on Sunday that two victims had died of burns sustained during the blast, raising the number of dead from the earlier figure of 39 to 41.
A thick column of black smoke continued to rise from the refinery on Sunday.
Firefighters said their work had been slowed down by increasing winds and a change in wind direction.
Mr Ramirez said fuel and oil supplies in Venezuela would not be affected as the state had a large enough stockpile to cover the shortfall.
Government officials said the blast occurred at 01:15 local time on Saturday when a gas leak created a cloud that ignited.
A committee has been set up to investigate the cause of the leak.