The incident, which took place shortly before 1pm on Thursday as a group of tourists watched with horror, caused significant damage to the bow of the vessel and the waterfront walkway.
Seven people were injured in the process, including three who were taken to the hospital according to San Diego Fire-Rescue Department Captain Joe Amador.
In the video taken by Steve Holden, who was standing on the docks at the time, about a dozen people can be seen waiting on the harbourside as the enormous vessel comes towards them to dock.
At first, it doesn't seem like anything is wrong but a couple of people duck out behind the barriers to distance themselves from the ship.
However, the ship's captain, who appears to no longer be in control of the vessel, starts blaring the horn in an attempt to warn the tourists still standing by the waterfront.
Chaos ensues as people dash to safety with someone shouting 'move, move'.
One pensioner seems almost oblivious as she continues walking by the water while the boat charges towards her.
A member of the public rushes to her aid, getting her out of the way just as the boat crashes into the pier.
The vessel only comes to a stop when it hits the barriers.
Some of those injured had to be carried away on stretchers according to Mashable though none of the injuries were life-threatening.
The accident was reportedly caused by a mechanical malfunction where a gear became stuck, which in turn prevented the 150-foot-long vessel from stopping as it approached San Diego's Embarcadero tourism area.
There was 144 people on board the Adventure Hornblower at the time of the accident.
The passengers stayed on board while a tugboat pulled the vessel away from the pier and re-positioned it so people could disembark.
Deb Ellis from the Phoenix area told The San Diego Union-Tribune that she was on the top deck when the boat crashed.
She said: 'We hit pretty hard.'
Deb and her husband, Mike Ellis, were taking the three-hour whale-watching cruise as part of the celebrations for her 60th birthday.
Mike Ellis, who was in the bathroom during the accident, said he was knocked against the wall.
Tables, chairs and people on the top deck fell down, according to the newspaper.
An investigation has been launched, which will be handled by the U.S. Coast Guard and harbour police