The court ruled on the Competition and Markets Authority's (CMA) ban on the train operator's MyFerryLink service.
In June Eurotunnel announced it was selling its two MyFerryLink passenger ferries, but retaining a freight ferry.
Now the company has announced its last ship, the Nord Pas-de-Calais, would be put up for sale.
The CMA said: "The Supreme Court has ruled that the Competition and Markets Authority (CMA) took the correct approach in assessing whether Eurotunnel's acquisition of three ferries and related assets formerly owned by SeaFrance should be treated as a merger."
The Eurotunnel Group said it was "extremely disappointed" by the decision.
"MyFerryLink had hoped to restart an activity with the freight-only ferry, Nord-Pas-de-Calais, which would have ensured 130 jobs," a spokesman said.
Eurotunnel is to abandon its plans to run freight-only ferry services between Dover and Calais after a Supreme Court ruling.