Tyrrell said the engineer worked for a subcontractor, Veolia, used by Metrolink since 1998, but had driven Metrolink trains since 1996. She said she believes the engineer, whose name was not released, was killed.
Authorities earlier announced 18 confirmed deaths in Friday's collision, but Los Angeles County coroner's Assistant Chief Ed Winter said that count did not include several bodies that could be seen but hadn't been reached in the lower level of a mangled two-story Metrolink passenger car.
The toll made it the deadliest U.S. passenger rail accident in 15 years.
Metrolink announced its determination of the accident's probable cause before investigators from the National Transportation Safety Board, leaders of the probe, made any public statements about the crash.
"Even if the train is on the main track, it must go through a series of signals and each one of the signals must be obeyed," Tyrrell told reporters. "What we believe happened, barring any new information from the NTSB, is we believe that our engineer failed to stop ... and that was the cause of the accident.
"We don't know how the error happened," she continued, "but this is what we believe happened. We believe it was our engineer who failed to stop at the signal.
"When two trains are in the same place at the same time somebody's made a terrible mistake," she said.
She said she didn't know if the engineer ever had any previous problems operating trains or had any disciplinary issues.
The Metrolink train, heading from Union Station in downtown Los Angeles to Ventura County, was carrying 220 passengers, one engineer and one conductor when it collided with the Union Pacific freight, with a crew of three, about 4:30 p.m. Friday.
The collision occurred on a horseshoe-shaped section of track in Chatsworth at the west end of the San Fernando Valley.
The crash forced the Metrolink engine well back into the first passenger car, and both toppled over. Two other passenger cars remained upright.
By late Saturday morning, the Metrolink engine had been pulled out of the mangled passenger car, which was raised by a crane and surrounded by tarps. Bulldozers pulled away chunks of metal.
Tyrrell, visibly shaking and appearing near tears as she spoke with reporters, said Metrolink determined the cause of the crash by pouring through dispatch records and reviewing computers.
Investigators quickly learned from those records that the commuter train, traveling along the main line, failed to stop for a red signal. Had the engineer obeyed the signal, she said, the accident would not have happened.
"We don't know how the error happened," she added.
Until Friday, the worst disaster in Metrolink's history occurred on Jan. 26, 2005, in suburban Glendale when a man parked a gasoline-soaked SUV on railroad tracks. A Metrolink train struck the SUV and derailed, striking another Metrolink train traveling the other way, killing 11 people and injuring about 180 others. Juan Alvarez was convicted this year of murder for causing the crash.
That was the worst U.S. rail tragedy since March 15, 1999, when an Amtrak train hit a truck and derailed near Bourbonnais, Ill., killing 11 people and injuring more than 100.
The Sunset Limited was involved in the worst accident in Amtrak's 28-year history. On Sept. 22, 1993, 42 passengers and five crew members died when the train plunged off a trestle into a bayou near Mobile, Ala. The trestle had been damaged minutes earlier by a towboat.