A handful of "Great Quake" survivors joined local politicians and residents in a pre-dawn ceremony re-enacting key moments of the event on Tuesday.
Gary Newsom, the mayor, joined fire and police chiefs in placing a wreath on the bronze Lotta fountain, as the hands of a large clock behind them neared 5.12am, the time the earthquake struck 100 years ago.
The crowd burst into a countdown, then blew whistles at the appointed minute. Police estimated a crowd of more than 10,000 people took part.
After a moment of silence, alarms sounded, church bells rang and a horse-drawn fire wagon raced along the city's Market Street to the fountain.
'City of doers'
Newsom told the crowd that the people of San Francisco "picked themselves up, dusted themselves off" and rebuilt in a "shining example" to New Orleans and other cities hit by natural disasters.
"We are a city of dreamers, a city of doers," he said. "Don't tell me you can't rebuild."
Most of the city's 400,000 residents were still in bed when the 7.8 magnitude earthquake struck on April 18, 1906.
Most of the city's residents were
asleep when the earthquake hit
The foreshock sent people scrambling, and the main shock arrived with such fury that it flattened crowded houses. The epicentre was a few kilometres offshore but was felt as far as the states of Oregon and Nevada.
The City Hall came crashing down after only 28 seconds.
Fires broke out and continued burning for days. Ruptured water pipes left firefighters helpless, while families carrying what they could fled to parks that had become makeshift mortuaries.
Historians say city officials, eager to bring people and commerce back to the city, underestimated the toll. Researchers are still trying to settle on a number, but reliable estimates put the loss above 3,000, and possibly as high as 6,000.
Historians agree that San Francisco will fall again in a future earthquake.
A study released on Monday determined that a repeat of the 1906 earthquake today would cause 1,800 to 3,400 deaths, damage more than 90,000 buildings, displace as many as 250,000 households and result in $150 billion worth of damage.
Linda Cain, 52, joined the crowd to honour her late grandmother, Loretta O'Connor, who lived through the quake.
"Growing up, she would talk about how this devastated her life," Cain said. "She loved San Francisco very much and she passed that on to me."
Philip Fradkin, author of The Great Earthquake And Firestorms Of 1906: How San Francisco Nearly Destroyed Itself, has chosen to make the Bay Area his home in spite of the threat.
"San Francisco fell, and it will fall again," Fradkin said. "And if we can't deal with the realities of history, we're lost."