Unai Emery announced Pierre-Emerick Aubameyang as Arsenal's new captain after the coach stripped Granit Xhaka of the armband following his recent outburst against supporters.
Xhaka, 27, swore at fans as he was jeered following his substitution in a 2-2 draw against Crystal Palace – also removing his shirt and cupping his ears.
He has since issued an apology of sorts, explaining that ongoing social media abuse aimed at his family also led to his furious reaction.
In the immediate aftermath of the incident, Arsenal said they would offer counselling and other support mechanisms as Emery said Xhaka was "devastated, sad and very down".
The Switzerland international sat out the following two draws against Liverpool and Wolves and did not travel to the Europa League clash against Vitoria on Wednesday.
In Guimaraes, Emery revealed he had taken the decision to relieve Xhaka of the captaincy.
"He is not today here, but also I think we need time with him and first protect him also to be calm and training with us every day," he said when asked about Xhaka's continued absence from the team.
"But I was speaking with him this morning and also I decided he is not one of the captains in our group. I decided that and I told him this morning.
"He accepted my decision. And also I told the other captains the decision. We need to carry on and focus for this match and next Saturday's match. I needed to make a decision and now it is closed."
Former captain Laurent Koscielny left under a cloud during the summer after refusing to travel on the club's preseason tour of the United States, eventually being sold to Bordeaux.
In response, Emery held a blind ballot among his players which saw Xhaka top the poll, and in a five-man leadership group Aubameyang, Hector Bellerin, Alexandre Lacazette and Mesut Ozil were also selected.
The Spaniard confirmed another vote will not take place and Aubameyang will lead the team, saying: "We have now Aubameyang, Hector, Lacazette and Ozil. They are the four captains and the first now is Aubameyang."
With Aubameyang left at home to rest, Bellerin is expected to captain the side in Portugal.
Despite revealing his decision over the captaincy, Emery dodged questions as to Xhaka's long-term future at the club.
"The decision I took I told him and I told the other captains and now it's continuing," he said after being asked three times if Xhaka had played his last game for Arsenal.
"Then, the time is giving us the next matches, the next weeks and months how we can continue with every player and with him also."
