Video from the Presidio showed Waymo vehicles lined up along roadways after fireworks launched from the Golden Gate Bridge.
Witnesses described seeing large numbers of autonomous vehicles stuck in traffic as crowds attempted to leave the area.
A witness to the gridlock who filmed the traffic mess, Jermaine Ellis said he saw approximately 20 Waymos get stuck.
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"People were saying that they were stuck in traffic for hours."
A second video taken in another part of the Presidio showed additional Waymo vehicles stopped in the street.
Waymo said in a statement: "On July 4th, extreme traffic congestion in Northern San Francisco disrupted normal operations for several Waymo vehicles."
Many people in the area reported losing cell phone service during the congestion.
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Phil Koopman, professor emeritus at Carnegie Mellon University who has spent more than 20 years studying autonomous vehicles, said communication disruptions can create challenges for autonomous vehicle operations.
"If there's no communications, it can't get the help, and it's stuck. But you also have a problem, they don't have that many remote assistants. It's a few dozen, so if 100 cars all get stuck at the same time, there aren't enough people to all get unstuck at the same time," Koopman said.
Waymo worked with officials to clear the vehicles, but some remained idle long enough that they had to be towed.
Separate video showed a Waymo vehicle carrying passengers driving over a lit firework.
Rose Peterson, a passenger traveling inside the Waymo braced herself as her vehicle drove over the exploding firework.
"The more me and my fiancé were talking about it, something really bad could have happened to us, something bad could have happened to the people around us. It was a very scary situation. Thinking about it still today, I'm really grateful to be here, honestly," Petersom said.
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That vehicle did not catch fire, but another unoccupied Waymo vehicle did, according to the report.
No injuries were reported in either incident.
Waymo said, "We take situations like this seriously and are committed to evaluating and learning from these events."
Peterson said the scene after the fireworks was particularly unusual.
"Oh my gosh, the long roads of San Francisco, it was just a row of Waymos. I didn't see a single normal car, it was crazy." she said.
The closure of the Golden Gate Bridge added to traffic challenges in the area, where large crowds gathered to watch fireworks launched from the bridge.
State law allows autonomous vehicles to be cited, though it was unclear whether any citations were issued in connection with the incident.