The 32-year-old was left out of Saturday's 3-0 win over Southampton, with sources having told ESPN he returned late from a sanctioned holiday, although both the club and manager Mikel Arteta refused to confirm the specific nature of the incident when questioned at the time.
A statement published on the Arsenal website on Tuesday morning read: "Following his latest disciplinary breach last week, Pierre-Emerick Aubameyang will no longer be our club captain, and will not be considered for selection for Wednesday's match against West Ham United.
"We expect all our players, particularly our captain, to work to the rules and standards we have all set and agreed. We are fully focused on tomorrow's match."
Arteta held prematch news conference on Tuesday, in which he refused to rule out a January departure for the striker.
It would not be the first instance of Aubameyang's poor timekeeping causing internal issues. In March, he was dropped for the north London derby against Tottenham Hotspur after arriving late for a team meeting on the day of a game.
A month earlier, the club had to speak to Aubameyang to "remind him of his responsibilities" after footage emerged of him getting a new tattoo despite strict COVID-19 protocol measures.
Although sources told ESPN that COVID-19 was not a key aspect of his latest breach, Aubameyang's delay in returning to the club may have had potential ramifications for the club's safety measures, especially at a time when Premier League guidelines have been tightened in response to the omicron variant surging through the United Kingdom.
The situation will also raise further questions over Arteta's relationship with Aubameyang and the striker's future at the club.
Aubameyang signed a new three-year contract worth an initial £250,000-a-week in September 2020 but has endured an alarming dip in form, having not scored since Oct. 22.
Asked by ESPN on Friday about rumours of a rift with Aubameyang, Arteta replied: "I have a very good relationship with my players. Everyone has to understand that I always do the best for this club and for this team. And often if that can benefit any individuals, I will always do it. The decisions are not personal; the decisions are just to get performance and the best out of the team. That's it.
"Obviously, when a player is not scoring it's affecting his confidence, it's affecting the mood and probably the belief, but you have to rebel against this situation, don't accept it and feel sorry for yourself."
Pushed on whether Arsenal were considering allowing Aubameyang to leave, Arteta added: "Really, we have never discussed something like this, and when players are under difficulty -- or the team is under difficulty -- what we have to be is supportive."
Aubameyang's demotion is another troubled day in the recent history of the Arsenal captaincy. His predecessor, Granit Xhaka, was stripped of the armband by former boss Unai Emery after telling Arsenal fans to "f--- off" as he was booed off upon his substitution in a Premier League game against Crystal Palace in October 2019.