The managing director of Connex, Olivier Brousse, said it was too early to say what had caused the incident but the company was taking it "very seriously".
It is thought the rapid intervention of signalman Les Hayes, 46, prevented the collision outside London's Victoria station at 2330GMT on Tuesday.
The near miss happened after a power failure set platform signals at the station to red.
The delayed 2310 Connex South Central train travelling from Victoria to Horsham in West Sussex was allowed to leave platform 19 and pass through a red light.
The trains were on a collision course but Mr Hayes spotted the danger and cut the power, stopping them within feet of each other.
Mr Hayes, from Basingstoke, Hampshire, said he had only done what any signaller would have done in the same situation.
He paid tribute to the other signallers involved, saying: "When I realised what could have happened ... it is very frightening.
"I am not a hero. It was a joint, team effort ... we all pull as one."
'Nasty incident'
Mr Hayes, an experienced signaller who has worked on the railways for more than 30 years, added: "I only did what I am paid to do - to prevent a very nasty incident.
"I gave permission for a train to come out of platform 19. While doing so, on platform 15 the East Grinstead train went by a red signal which was indicated by the track circuit lights flooding.
"As soon as we realised there was a problem we sent an emergency stop message to the drivers and ordered the power to be switched off to make sure the trains stopped."
Michael Holden, director Railtrack Southern, paid tribute to the actions of Mr Hayes and his team, as well as the driver of the Horsham train who quickly applied his brakes.
Both services were travelling slowly, but were full of passengers that had been caught up in earlier delays on the line.
Railtrack, Connex and the Health and Safety Executive have all launched investigations into the incident.
In a statement Railtrack said: "Despite the low speeds, any collision would have been very, very serious and a full and thorough investigation has started."
The managing director of Connex, Olivier Brousse, said it was too early to say what had caused the incident but the company was taking it "very seriously".
Passenger Roger Wicks, who was travelling on the East Grinstead service, said that passengers were not told after the incident that they had been in any danger.
He said he had been left with an "uneasy" perception of the rail network after the incident, saying: "It could have been so much worse.
"We got about 200m before the driver jammed on the brakes and all the power went."