Remarkably, the 37-year-old striker did not feature in the last 16 meetings on Tuesday, and his replacement, Goncalo Ramos, scored a hat-trick in a 6-1 win.
Ronaldo appeared from the bench, but a report in Portuguese publication Record said the striker had previously threatened to leave in a tense conversation with manager Fernando Santos.
“The FPF clarifies that at no time did the captain of the Selecao, Cristiano Ronaldo, threaten to leave the team during his stay in Qatar,” the federation said.
“Every day Ronaldo builds a unique career at the service of the national team and the country, which must be respected.
The FPF said Ronaldo’s appearance against Switzerland was yet another demonstration of his commitment to the cause.
Ronaldo is the Portuguese player with the most caps and the top male international scorer of all time.
The five-time Ballon d’Or winner did not train with the other substitutes on Wednesday after the match, instead taking part in a gym session alongside the starters against Switzerland.