Fernando Santos’ side went into the match in Lancy as the favourites.
They won 4-0 when the sides met at Estádio José Alvalade just a week ago.
But Switzerland managed to get revenge as they won 1-0.
Switzerland took the lead after just 56 seconds when Haris Seferovic found the back of the net.
There were no further goals as Switzerland held on to clinch a narrow victory in front of their own fans.
Bruno Fernandes played 74 minutes in his side’s defeat.
The Manchester United midfielder is known to lose his cool when things aren’t going well for his side.
And he lost his head once again in the latter stages of the match.
In the 91st minute, the referee gave Switzerland a free-kick after a coming together between Nico Elvedi and Andre Silva.
Portugal’s players were furious. They thought that Elvedi had gone to ground too easily.
And Fernandes, who was on the bench at the time, was also livid.
The camera panned to him and he appeared to shout an expletive or two at the direction of Switzerland’s bench.
Watch the moment below…
It’s fair to say that Fernandes was not impressed at all.
Portugal have now slipped to second place in League 1, Group B following the defeat.
They find themselves one-point behind Spain with two group games remaining.
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Switzerland, meanwhile, are still bottom of the group but are now just one-point behind Czech Republic in third.
The final two games in the group will be played at the end of September.