Fernandes scored a brilliant goal during the clash in Porto, and the result confirmed Portugal's position at the top of Group 1 of League A, with the team advancing to the quarter-finals of the competition.
The Man United captain picked up a milestone booking during the contest, though, and he has therefore been released from international duty ahead of Portugal's final game in the section against Croatia on Monday.
Portugal head coach Roberto Martinez revealed during his post-match press conference on Friday that Fernandes had been removed from the squad alongside Bernardo Silva, Pedro Neto and Cristiano Ronaldo.
"In the first stage, we made six changes from one game to the next," Martinez told reporters.
Man United captain Fernandes has been released from Portugal duty
"It's important for us to be first - and we already are. We need to be competitive to add to the group, it's getting harder and harder to get into the starting eleven. There's a World Cup finals in 18 months.
"The game against Croatia is important, we need to look at other players. We're going to let go of Bernardo Silva, Pedro Neto, Cristiano Ronaldo and Bruno Fernandes, who is suspended - so we're going to call up Fabio Silva and [Geovany] Quenda from the Under-21s."
Fernandes will therefore be able to resume training with Man United in the early stages of next week, with the Red Devils returning to Premier League action against Ipswich Town on November 24.
Ruben Amorim's preparations for that match will be difficult due to the number of players away on international duty, but Fernandes' early return is excellent news for the club's new head coach.
Will Fernandes be a key player for Amorim?
Amorim stopped short of confirming that he is planning to use a 3-4-3 system at Man United in a wide-ranging interview with MUTV, but that is expected to be the case, starting against Ipswich next weekend.
Fernandes, in that formation, would be used as one of the number 10s, and it is believed that Amorim views the 30-year-old as central to his plans at Man United moving forward.
The Portuguese struggled for form in the early stages of the campaign, but he has scored four times and provided two assists in his last four appearances for the 20-time English champions.
Amorim is expected to take Man United training for the first time on Monday, and Fernandes could now be a part of that group, but his teammate Diogo Dalot has remained with the Portugal squad for their game against Croatia.