In January, the company was told it must quit the cross-Channel ferry market following a ruling by the Competition Appeal Tribunal.
But Court of Appeal judges overturned the decision by a majority of two to one on Friday.
MyFerryLink, which has been operating the service since 2012, described it as a "momentous victory".
Raphael Doutrebente, of MyFerryLink, said the decision should "spell the end of the road" for the Competition and Markets Authority's (CMA) "attempts to suppress" its cross-Channel service.
"The decision of the Court of Appeal is very comprehensive, exposing fatal flaws in the CMA's analysis," he added.
"The decision represents a significant victory both for our dedicated employees and for our customers, who will continue to benefit from healthy competition on the short sea route."
MyFerryLink has been running up to 24 daily crossings on the Dover-Calais route using three former SeaFrance ships that Eurotunnel bought when the operator went bust in 2012.
The CMA claimed Eurotunnel had more than half the market share of Channel crossings when its rail link and ferry operations were both taken into consideration.
In a statement the CMA said would "study the judgment carefully and consider its next steps".
Eurotunnel's MyFerryLink has won its legal battle to overturn a ban on it operating between Dover and Calais.