The South Americans have been deducted three points in qualifying for the 2026 tournament after the use of false information to obtain a passport for a Colombia-born player.
Chile and Peru had argued that Ecuador used an ineligible player in eight qualifying games and should be thrown out of the World Cup.
But the CAS judges said Ecuador defender Byron Castillo was eligible by FIFA rules to play in both the qualifying campaign and at the World Cup in Qatar.
However, the judges also said Castillo was born in Colombia and that false information about his date and place of birth had been used to get an Ecuadorian passport.
CAS imposed a 100,000 Swiss francs (£88,000) fine on the Ecuador federation and ordered a three-point deduction in the South American qualifying group for the 2026 World Cup.
Additional reporting by AP.