A club spokesman said Aubameyang had committed a "breach of prematch protocol." Sources told ESPN the forward had reported late to the training ground this morning for the game, which Arsenal won 2-1.
The club refused to elaborate on the situation when contacted by ESPN for further comment, but Arteta said Aubameyang was due to play before a late unspecified breach.
"He was going to start the game, we had a disciplinary issue, we've drawn the line, we move on," he told Sky Sports. "We keep it internal. We have a process that we have to respect for every game, and that's it."
Asked whether he debated axing the 31-year-old from the squad altogether, Arteta added: "It is a decision made after evaluating everything, and who Auba is and what's he done and that's it."
Aubameyang was the subject of an internal investigation over a possible COVID-19 breach in February when footage emerged of the striker getting a tattoo.
The club confirmed to ESPN at the time that talks were planned with Aubameyang to "establish the facts," but it is unclear whether this latest incident is related. Aubameyang has started six of Arsenal's seven games since the tattoo footage emerged.
Alexandre Lacazette was drafted into the starting line-up against Spurs and given the captain's armband for the match, in which Arsenal closed the gap behind their rivals to four points.
Lacazette scored the winner from the penalty spot for Arsenal, and after the match, Arteta praised Aubameyang's character.
"He is an incredible guy and one of the most important players in the team," the Arsenal boss said. "He is our captain and these things happen.
"We have lots going on in our lives and people finding it hard with the restrictions. I will never tell anything that happens in the dressing room."