The ruling overturns a ban on the Channel Tunnel operator's Dover to Calais ferries which had been imposed by Britain's anti-monopoly regulator.
The Competition and Markets Authority (CMA) said in a statement it would "study the judgment carefully and consider its next steps", while MyFerryLink hailed the ruling as "a momentous victory".
The CMA last year ordered Eurotunnel, which operates the undersea Channel rail tunnel between France and England, to stop running its ferry service on grounds of unfair competition.
The MyFerryLink brand came into existence after Eurotunnel in 2012 acquired the three ferries and related assets of SeaFrance.
The ruling said that the CMA was not legally competent in the case as there had not been a formal merger between Eurotunnel and MyFerryLink.
MyFerryLink, which employs some 533 people in France and 71 in Britain, operates up to 24 daily crossings between Dover and Calais.