The Portugal international picked up two yellow cards during the pulsating 3-3 draw in Portugal, with the second of those arriving for a high boot, and it proved to be the second time in five days that he was sent off.
Indeed, Fernandes also saw red during Man United's 3-0 loss to Tottenham Hotspur in the Premier League last weekend, which was due to lead to a three-game domestic suspension.
However, the club successfully appealed the decision and were able to overturn the ban, which would have ruled him out of the league fixtures with Aston Villa, Brentford and West Ham United.
Fernandes will have to serve a suspension for his red against Porto, though, despite the fact that there was minimal contract on Porto defender Nehuen Perez.
Fernandes will be suspended against Fenerbahce in Europa League
The Red Devils captain will therefore be suspended for Man United's third match of the 2024-25 Europa League, which comes against Jose Mourinho's Fenerbahce side on October 24.
Having received two yellow cards rather than a straight red, it will only be a one-game European ban.
"As a rule, a player or team official sent off by the referee is automatically suspended for the next match in a UEFA club competition (i.e. UEFA Champions League, UEFA Europa League, UEFA Conference League or UEFA Super Cup)," state UEFA rules.
"In the event of a serious offence, the UEFA Control, Ethics and Disciplinary Body is entitled to augment this punishment, including by extending it to other competitions."
However, UEFA are highly unlikely to consider it to be "a serious offence", meaning that Fernandes will be available against Villa this weekend, while his next European appearance should come against PAOK on November 7.
Man United secured late point against Porto despite Fernandes red
Man United led 2-0 against Porto before trailing 3-2 in the second period, but they secured a late point in Portugal, with Harry Maguire netting a last-gasp header in the European contest.
"We started the game very good, we dominated, scored two good goals, but then we lost control. So the start was good, the middle part was not good, and then we finished very good," Red Devils head coach Erik ten Hag told TNT Sports after the match.
"It's a tough place to go, so coming back from 3-2 we get the equaliser, which is good for the spirit. You see again that the team has a really strong character, but the middle part, the defending, we have to improve.
"First of all, we must be better on the ball. [We needed to continue] like the first part: keep switching where we had our free players. We had a good plan - in our half-spaces we had our free players. So use them and more goals will come.
"We had three clean sheets not so long ago, so we can defend very good. But we have to go back to those habits. Only then can you win games. When you score three times in an away game in Europe, it must be enough."
As well as Fernandes, Kobbie Mainoo should be available for Sunday's trip to Villa despite missing out against Porto on Thursday due to an issue that he sustained against Tottenham.