SAS had sought to reduce the 47.5 million dollar fine imposed by the European Commission in 2001.
The Commission imposed fines on both companies after finding they had concluded a secret agreement to share routes in and out of Denmark.
SAS had accepted the ruling, but contested the size of its fine. The airline group is not expected to appeal further.
News of the outcome of the appeal comes after the government here chose Scandinavian Airlines to exclusively supply the Swedish state with domestic flights on 52 routes.