Granit Xhaka has been stripped of the Arsenal captaincy following his extraordinary fall-out with a large section of the club’s fans, Unai Emery has confirmed.

The manager has chosen to draw a line under a situation that has cast a damaging cloud of uncertainty over the club ever since Xhaka, dismayed at the negative reaction when he left the field against Crystal Palace on 27 October, removed his shirt while swearing and gesturing towards the support. Pierre-Emerick Aubameyang will be the new captain and Xhaka’s future at the club beyond January now looks in serious doubt.

“I was speaking with him this morning and I decided he is not one of the captains in our group,” Emery said as he prepared for Wednesday’s Europa League match with Vitória Guimarães.

Emery did not offer a specific reason for his decision, although there is no doubt the situation had become untenable. He had advised Xhaka to offer a swift public apology in the immediate aftermath but the midfielder stopped short of doing that when he broke his silence last Thursday.

Xhaka said social media threats towards his family had brought him to “boiling point” and apologised for any disrespect felt by “the group of fans that support our club with positive energy”. The intervention did little to move things on and it was clear the situation would not resolve itself without decisive leadership from above.

“He accepted my decision,” Emery said. “And also I told the other captains [Aubameyang, Héctor Bellerín, Alexandre Lacazette and Mesut Özil, in that order] the decision. We need to carry on the focus for tomorrow’s match and next Saturday’s match [against Leicester].”

Xhaka was not in the group that travelled to Portugal, although that would ordinarily have raised few eyebrows given Arsenal sit top of Group F with nine points and their opponents are yet to get off the mark.

Emery, who has been keen to put Xhaka’s mental wellbeing at the forefront of the past week’s discussion, said Arsenal “need time with him to be calm and training with us every day”, but it is increasingly hard to see the player remaining in north London beyond the short term.

“It is clear there are not more words about that,” Emery said when asked whether Xhaka had asked to leave the club. “I told him the decision I took, and I told the other captains. Then time is giving us the next matches, the next weeks and months, and how we can continue with every player and him also.

“For me it’s finished. His future with us is coming for the next weeks or the next months. Now we need to be focused for tomorrow.”

Whether Xhaka will play for Arsenal again, Emery offered no direct response and said the club have needed to “take some decisions about some circumstances that have happened”. But it is difficult, at this point, to see when Xhaka might be eased back into the fold, given Arsenal’s league form has faltered badly and the manager is under growing pressure.

The game at Leicester, which will now be critical against a side who appear to have outstripped Arsenal, hardly looks cut out for a Xhaka recall. There had been a school of thought that a substitute appearance in Portugal, in a relatively low-profile tie far from London, might be a logical first step in his rehabilitation.

Instead Xhaka will watch from home and Bellerín, who tweeted his support for Xhaka last Monday, is expected to be captain against Vitoria. “He made a mistake but as a dressing room we have to be together,” said Bellerín, this time speaking alongside Emery. “These things happen and that’s it. We back him. He is playing his part now. We respect the players, we respect the decision of the coach and the club. For us it’s just to give him our love and care. He’s one of us, so we’re just helping him get through it.”

Wednesday’smatch will kick off at the unusual time of 3.50pm (UK time) due to nearby Braga’s staging of a home match in the same competition on Thursday. Aubameyang and David Luiz have also stayed at home but Nicolas Pépé could start after spending Saturday’s draw with Wolves on the bench.