The Italian finished the match in an unfamiliar position on the left wing, with Noni Madueke moving to left-back as Mikel Arteta adjusted his side during the closing stages.
Calafiori had come off the bench for the second half and appeared uncomfortable towards the end of the game. He went straight down the tunnel at full-time, leaving Arsenal to await further clarity over the problem.
Arteta played down the initial concern but acknowledged that the defender had experienced an issue.
“Yeah I wasn't that mad to change those two from their positions.
“It was because he [Calafiori] had a slight issue, we don't know what it is, it seems to be something very small, but he was cautious about it.”
The comments offer some initial reassurance, although the precise nature of the problem has not been established. Calafiori had also taken a heavy collision around the ribs during the match, but it remains unclear whether that incident was connected to his discomfort.
The defender had been available for every match this season after completing a full pre-season. Arteta had indicated before the Everton game that Calafiori was ready to start, but opted to begin with Myles Lewis-Skelly instead.
“Yeah, he's ready. I think Ricci is in a different place because he had a full pre-season as well. And he's been available for every match. And Piero, he's trained with us and is available for tomorrow as well.”
Arsenal also had a concern over Gabriel Magalhaes earlier in the match. The Brazilian appeared to jar his knee during an awkward landing and received medical attention, prompting fears that he might have to come off.
However, Gabriel continued and scored Arsenal's second goal in the 68th minute, heading in Ben White's cross at the far post. His contribution helped secure a 2-0 victory that moved the champions level on points with Manchester City.
Arteta later praised the defender's determination, explaining that the reaction of his teammates had initially made the incident look worrying.
“We all [thought he would have to come off] by the reaction of his team-mates. It was a really worrying action. We know Gabi and how tough and strong he is - and he seems to be OK.”
Arsenal will hope Calafiori's issue proves minor, but further assessment will be needed before his availability for the next fixture can be established.