A fire official said one train was unloading passengers when the second train ran into it at an estimated speed of 15 to 20 miles per hour injuring about 16 people.
The train was traveling an estimated 15 to 20 miles per hour when it struck the stationary Amtrak passenger train about 10 p.m., said Oakland Fire Department battalion chief Emon Usher.
Most of the injuries were minor, but several people were taken to local hospitals, Usher said.
Amtrak spokesman Cliff Cole described the crash as it as a "low speed" collision between Amtrak's "San Joaquin," a train that operates between Bakersfield to Oakland, and the Coast Starlight, a train from Los Angeles to Seattle
He said the wheels of each lead engine went off the track.
Authorities said there were injured on both trains, but there was no breakdown on how many from each.
Alton Smith, a passenger on one of the trains, told television station KTVU that he felt "an awful jolt" from the impact.
About two hours after the crash, about 50 passengers were gathered inside the train terminal, talking to Amtrak officials, while Amtrak and local officials inspected the two trains.
There was no immediate word on what caused the crash, which is under investigation.
Amtrak officials said train traffic has been temporarily suspended at the station.
Passengers who paid for travel on canceled trains can contact Amtrak to receive refund without fee or penalty, according to Amtrak.
The crash is the second significant incident in two weeks in the San Francisco East Bay area where there were injuries to Amtrak passengers.
On Sept. 30, 37 passengers and two crew members suffered minor to moderate injuries when an Amtrak passenger train collided with a truck at a crossing near Brentwood where there were no lights or gates.
The driver of the truck and a passenger inside were not hurt.