FIFA have opened disciplinary proceedings after the two players, who are of Kosovar heritage, celebrated with a gesture which appeared to imitate the eagle displayed on Albania’s flag.
"Anyone who experience the electric atmosphere of the game can appreciate more the performance of our national team and can understand the emotions which overcome a player," Defence, Civil Protection and Sports minister Guy Parmelin told the Neue Zurcher Zeitung (NZZ).
Swiss Foreign minister Ignazio Cassis was also sympathetic.
"I have no doubt that you can feel patriotic emotions for the land which has taken you in without forgetting your roots," he said.
FIFA's disciplinary regulations state that players found guilty of provoking the public face a two-match suspension and
Swiss Football Federation president Peter Gillieron said he was hopeful that the pair would be absolved.
"It would be a hammerblow if they were to be suspended," he said.
Serbia refuses to recognise the independence of its former province Kosovo, whose 1.8 million people are mostly ethnic Albanians, which broke away 10 years ago.
Both FIFA and its European counterpart UEFA keep Serbia and Kosovo apart when making the draw for international competitions.
Switzerland have four points from their first two games in Group E and need a draw against Costa Rica in their final game to progress to the round of 16.