The train from Paris was bound for Waterloo International but sent towards Victoria station at about 2230 BST on Monday.
The driver noticed the error seconds after passing a green signal and stopped the train, before being allowed to reverse and return to the correct route.
Railtrack said there were no safety risks and the signaller would be interviewed.
Off track
The train would have been travelling at up to 40 mph when it was sent along the wrong track at a busy junction two miles south of Waterloo, a Eurostar spokesman said.
The train was due in Waterloo at 2246 BST.
It arrived safely at Waterloo approximately 25 minutes late.
A Railtrack spokesman said: "We know what happened.
"There was nothing unsafe about this. He just sent the train in the wrong direction.
"There is nothing to investigate other than interviewing the signaller concerned."
He said there was no risks to passengers and said it was like police putting up wrong diversion signs on roads.
In a statement, Railtrack said: "The driver of the train quickly realised the routing error, stopped and was given permission to reverse his train and take the correct route into Waterloo.
"There was absolutely no safety risk.
"As is normal practice, the signaller was relieved from duty at the time will be dealt with through normal internal procedures."