The visitors had been trailing 1-0 at the break, but substitutions inspired a comeback to win 2-1 in Berne with goals from Bruno Peres and Marash Kumbulla.
“The important thing is to have faith in all your players," Fonseca told Sky Sport Italia.
“There's still a long way to go in the group and the season. We rested a few players and can now focus on Milan in Serie A.
“I am glad that those who hadn't played for a while gave such a good response when called upon. It's very pleasing."