Seemingly miraculously, no one was reported killed by the blast at Caribbean Petroleum Corp. in the suburb of Bayamon. The cause was unknown.
The explosion at 12:30 a.m. was the equivalent of a 2.8 magnitude earthquake, according to the Puerto Rico Seismic Network.
It shook people out of bed across metropolitan San Juan and shattered windows across the bay in colonial Old San Juan, one of many neighbourhoods where onlookers gaped at the thick smoke boiling north toward the Atlantic Ocean.
Gov. Luis Fortuno declared a state of emergency for five municipalities, including San Juan and Bayamon, to receive federal funds for affected areas. Up to 1500 people were evacuated from one neighborhood because of concerns over smoke contamination, he said.
Fifteen of the site's 40 fuel tanks caught fire, but several tanks were no longer burning by Friday night, Fortuno said.
He said Puerto Rico still has a 24-day supply of fuel and assured residents six of the US island's seven fuel lines were operating.
The fire was contained, chief firefighter Pedro Vazquez said, and firefighters were spraying the rest of the fuel tanks at the facility with cold water and foam to reduce the risk of further blasts.
Fortuno said at least four people sought help for respiratory problems. Several drivers were hurt when the explosion shattered glass in their cars and two people suffered minor injuries at the U.S. Army's Fort Buchanan, adjacent to the fuel storage site, which supplies Gulf gas stations across the island.
Gulf spokeswoman Frances Rios said all five workers who were inside the plant managed to escape without injury after realising what was happening.
"They were able to get out of the place quickly," said Rios, who is based in San Juan. She said the company's facilities had been well maintained and it woudl be impossible to determine the cause of the blast before the fire was extinguished.
Marcial Orlando Felix, the top local official for the U.S. Bureau of Alcohol, Tobacco, Firearms and Explosives, said a special team from the mainland would investigate the blast but would have to wait until the fire was out to enter the site.
Police and FBI agents were investigating graffiti found after the blast in a highway tunnel in the capital with the message: "Boom, fire, RIP, Gulf."
"Everything is very preliminary at this point but obviously we're looking into the graffiti and it's a concern," Figueroa Sancha said.
The tanks at Caribbean Petroleum hold about 10 percent of the gasoline consumed in the U.S. Caribbean territory, Consumer Affairs Secretary Luis Rivera Marin said. He said there was no risk of shortages, but the government ordered gasoline prices frozen anyway after some service stations raised prices.
The flames, which could be seen from miles away, intensified in the hours following the explosion and police chief Jose Figueroa Sancha said it would likely take several days to put out the fire.
The U.S. Federal Aviation Administration diverted plane traffic because of the smoke.
At a nearby top-security prison, armed guards stood watch as the first of the 2,400 inmates were loaded onto buses for prisons elsewhere on the island.
Experts from the Environmental Protection Agency were traveling to Puerto Rico to help monitor the capital's air quality. In the meantime, environmental authorities urged people living near the plant to keep their windows shut.
