Earlier witnesses reported hearing several explosions from the tank at the centre of the fire.
At one point, flames were seen reaching more than 100m, while hundreds firefighters backed up by soldiers were brought in to tackle the blaze.
Anang Rizkami, a spokesman for Pertamina, told local radio the tank holds about 5 million litres of regular gasoline and distributes about 100,000 barrels of fuel to the Indonesian capital every day.
|Pertamina said the fire would not affect supplies of fuel to Jakart [EPA]
The blaze sparked panic buying at some petrol stations, but Pertamina officials denied that the fire would lead to shortages.
"Our fuel stock is enough, for now we do not need additional imports," Iin Arifin, Pertamina's vice president director, told the Associated Press.
He also said that Pertamina had set up an investigation team to determine the cause of the fire.
Last year, police uncovered a plot to blow up the oil depot, and detained five men who they said were members of Jemaah Islamiyah, the South-East Asian group Indonesian authorities say has links to al-Qaeda.
The group has been blamed for several attacks in the region, including the 2002 Bali bombings where 202 people were killed.
Earlier this month Pertamina was publicly reprimanded by Susilo Bambang Yudhoyono, the Indonesian president, following widespread complaints about fuel shortages in the capital.