The flames were put out in the three fuel tanks that had been ablaze at the Amuay refinery, officials said. Television images showed one tank still smouldering.
Oil Minister Rafael Ramirez said officials expect to restart operations at the refinery in two days.
The fire took longer to put out than officials had initially hoped. Ramirez had said Saturday the state oil company would be able to restart the refinery "in a maximum of two days," then later said it would be two days once the fire was out.
"This fire has been extinguished and now of course come all of the subsequent jobs: evaluation, securing the entire area," Ramirez told the Caracas-based television network Telesur. He said firefighters were still working in the area spraying the tanks with foam to cool them down.
"We need to check all the lines, all the connections, all the valves," Ramirez said. He said the disaster hadn't affected the refinery complex's capacity to process up to 1.2 million barrels a day although those operations have stopped while the fires raged.
The explosion early Saturday morning at the refinery killed at least 41 people and injured more than 150, Prosecutor General Luisa Ortega said.
Officials have said a gas leak led to the blast, but investigators have yet to determine the precise causes.
President Hugo Chavez had announced initial progress in fighting the blazes late Monday, saying in a message on Twitter that one of the tanks had been extinguished. That came after officials said earlier in the day that the fire had spread to a third tank.
Amuay is among the world's largest refineries and is part of the Paraguana Refining Center, which also includes the adjacent Cardon refinery. Together, the refineries usually process about 900,000 barrels of crude per day and 200,000 barrels of gasoline.
Criticisms of the government's response to the gas leak came from the refinery's neighbours as well as oil experts. Residents said they had no official warning before the explosion hit at about 1 a.m. on Saturday. The blast knocked down walls, shattered windows and left streets littered with rubble.
On Tuesday, residents said they were relieved and talked animatedly with their neighbours.
"We feel happy after so many days of anguish and fear," said Hilda Castellanos, a housewife who said the flames had been diminishing since hours before dawn on Tuesday.
Edgar Medina was working with his father to clear rubble that blocked the way to what remained of their windowless home. "Now what we hope is that they help us rebuild everything."
Chavez visited some of the wounded in a hospital on Monday and said that more than 500 homes were damaged.
Officials said at least 20 of those killed were National Guard troops who had been stationed at a post next to the refinery.
The disaster occurred little more than a month before Venezuela's upcoming Oct. 7 presidential election. Opposition candidate Henrique Capriles said on Monday that the tragedy shouldn't be politicized, but he also strongly criticized a remark by Chavez, who had said "the show should continue, with our pain, with our sorrow, with our victims."
"It seems irresponsible, insensitive ... to say 'the show should continue,'" Capriles told reporters in Caracas. He repeated past criticisms about the number of accidents at the state-owned oil company, and called for "a serious, responsible and transparent investigation."
"The state has to give answers. Venezuelans have a right to know what happened in Amuay," Capriles said.
Associated Press writer Fabiola Sanchez in Caracas contributed to this report.