The fire, which was reported around 4:40 a.m., was considered contained as of 11:30 a.m.
A total of 150 firefighters and 50 fire apparatus responded to the scene. One firefighter was injured in the fire with a severe laceration to the hand and transported to a local hospital.
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The flames were intense, jumping 100 feet into the early morning sky and a rear portion of Pier 45, fully engulfed.
VIDEO: Bright flames, huge smoke plume visible in SF
VIDEO: Bright flames, huge smoke plume visible in SF
People from across the city captured video of the blaze which started in the early morning and 150 firefighters were battling to put it out.
"Unfortunately, this building is a complete loss, all four corners collapsed inward, " said SFFD Lieutenant Jonathan Baxter.
The fire left haze and plumes of smoke over San Francisco and could be seen from other parts of the Bay Area.
The SFFD says the fire was burning above and below the historic pier, made of concrete and wood, built in 1926.
PHOTOS: 4-alarm fire at San Francisco's Fisherman's Wharf
There were tense moments on the Bay as the fireboat St. Francis fought to save the historic WWII ship, the SS Jeremiah O'Brien from ruin. She was docked just feet from the fire.
"If there's anything positive, we were able to save the Jeremiah O'Brien, now with more emphasis on Memorial Day," Baxter added.
The ship, which is one of two remaining fully functioning Liberty ships launched during World War II, stormed Normandy on D-Day in 1944. The ship docks by the pier and is a popular tourist attraction.
"Our firefighters absolutely saved the SS Jeremiah O'Brien during this fire as flames were pinching on the side of this vessel," said Baxter.
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The ship's captain was beyond grateful.
"It sounds corny but that was my reaction - it's a miracle, that's because of the fire department, " said Capt. Cavan Lesieur.
VIDEO: SFFD Lt. Baxter gives update on Pier 45 fire
San Francisco Fire Department official gives update on Pier 45 fire
A seafood distributor at Pier 45 said on Instagram Saturday morning that the fire has caused about $15,000 in damage. The fire damaged trucks and equipment at Water2Table, which receives and distributes fresh fish to Bay Area businesses.
Joe Conte with Water2Table spoke to ABC7 and said the fire could be "disastrous for the local fishing community."
Conte said because of the COVID-19 pandemic, Water2Table is distributing food directly to consumers.
"This is critical," he said, adding that there are about 15 businesses like Water2Table along the wharf.
VIDEO: View from SKY7 of a 4-alarm fire burning at a warehouse at Pier 45 in San Francisco
VIDEO: SKY7 view of a 4-alarm fire burning at a warehouse at Pier 45 in San Francisco
He adds that fish from Fisherman's Wharf is shipped state and nationwide.
"I'm hoping we can get on to that pier soon," he said.
Conte said another concern is that the power is out along the pier. He said there is "millions" of dollars worth of fish in facilities along the pier.
Mitch Gronner works for Aloha Seafood. He was inside the warehouse when the fire broke out and said it was only the size of a camp fire, and then exploded.
"It means a loss day of business, a lost good day of business," Gronner said. "It means a lot of restaurants and a lot of our home delivery customers aren't going to be able to be doing what they were planning on doing for Memorial Day picnics or BBQ's or whatever."
Randy Quezada, Director of Communications for the Port of San Francisco, said Pier 45 has four structures, which are called A, B, C and D sheds. C was destroyed. Quezada said there was still power in some parts.
"We didn't lose B and D where the fish processing units are. In fact we didn't lose power which is important. So any fish they had to keep on ice is still cold," Quezada said.
He said since the integrity of the pier is still up in the air, boats that would normally come and unload their catch need to hold onto them for a couple more days.
"We do know this area is critically important and we want to work with the fisherman, we want to work with everyone in the area to bring the area back, but in order to do so we need to do it safely," Quezada said.
The fire destroyed corporate office space for Red and White Fleet, a family owned tour boat company since 1892.
Tyler Foster, Executive Vice President of the Red and White Fleet, said it felt surreal to get the call at 4:45 a.m. that the pier was on fire.
"It sort of feels like the triple whammy," Foster said.
They ceased operating their boats on March 16 under the shelter-in-place order.
"We, unfortunately, had to let go of the majority of our staff shortly thereafter. And now this. We'll get through this, what we really need is to get back out on the Bay and get people back on the Bay again," Foster said.
He said once they get to reopen, it will be up to San Franciscans and locals to go out onto the water.
"We're trying to understand where we sit in the phasing. What we do is an outdoor activity. We take people out on the Bay and the air doesn't get fresher," Foster said.
RELATED: Here's what it will take to reopen the Bay Area
It's unclear what ignited the flames and investigators are now working to learn the cause and origin of the fire. Officials are looking at surveillance footage.
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According to Baxter, evacuations were underway at adjacent commercial warehouses during the fire and his crews were evacuated when walls began collapsing in the warehouse during the fire fight.
"To our knowledge nobody is supposed to be in the building and we are hoping that there is no victim," he said.
The warehouse, which holds fish processing equipment and a few offices, is typically unoccupied at night. But Baxter notes homeless people have been seen in buildings and warehouses in the area.
Authorities are also looking at the structural integrity of the pier to make sure it is safe.
SF officials give update on 4-alarm fire that threatened WWII ship
Crews battle 4-alarm fire at SF's Pier 45