Managing director Ryan Flaherty said he was "very proud" of the team manager for hitting the emergency brake that stopped the train after it overshot Waverley Station in Edinburgh yesterday.
The manager is understood to have acted as the train "flew" through the station without stopping.
The commendation came as the Office of Rail and Road regulator launched an investigation into the incident.
Mr Flaherty said operator Serco's own early investigation indicated it was caused by an "isolated operational mistake" involving the London-Edinburgh/Glasgow service.
It is understood the train's braking system was not reset correctly when it was divided from a portion for Glasgow at Carstairs in South Lanarkshire.
A photographer, who took a picture of the train as it went into a tunnel at the east end of Waverley, tweeted later: "I am with four passengers who were in the vestibule behind the loco of this train who saw the guard run into his office, press the red button, nothing happened, then ran out of his office to press another red button on the left hand side door.
"This immediately stopped the train."
One of those passengers, Andy Picton, an off-duty engineer with South Western Railway, confirmed: "Was stood in the vestibule in the coach behind the loco as we flew through Waverley.
"Don't think the loco stopped us, as the guard hit the emergency stop right by us and only then did we come to a halt, that after hitting the one in the guard cabin that didn't seem to work.
"Driver realised there was an issue as he approached Haymarket and couldn't slow down. Unsure if guard aware of prob at that time.
"Was quick thinking by the driver, who phoned through to the signaller as we went through Haymarket and got the route through Waverley cleared to avoid anything more serious. Hats off to him!"
Mr Flaherty said: “We are very proud of our train manager who followed the correct processes and deployed the emergency brake to bring the train to a stop during yesterday’s incident at Edinburgh Waverley.
“Our own early investigation indicates there are no technical or safety concerns with the rolling stock and that this was an isolated operational mistake.
“Following the incident, our new trains ran as normal last night and will do so again this evening.
We will continue to work with the relevant authorities to investigate the underlying cause and expect to provide an update next week.”
The UK Department for Transport's Rail Accident Investigation Branch (RAIB) has still to decide whether to launch its own investigation
A spokesperson said: "An RAIB inspector was deployed yesterday to gather evidence.
"We will use this information to decide any further course of action.”