Allen suffered concussion after taking a blow to the head in Wales' 1-0 defeat to the Republic of Ireland and he was forced off at the Cardiff City Stadium.
He was checked over by the Potters' staff on Thursday but boss Mark Hughes has admitted the former Liverpool man has had a tough few days.
"Joe's not great; we've given him a couple of days just to stay at home," Hughes said. "He came in yesterday (Thursday), felt a lot better, but I think the reality is he's unlikely to be available unfortunately.
"Clearly concussion's a thing you can't take any risk with, we've got to follow the protocol. Hopefully he'll start to show some improvement and be ready to come back and train at some point next week. He's not going to be available this week.
"He was allowed home but he had a bang to the head. He found it difficult to remember the incident itself - that tells you where he's at in terms of the severity of it.
"We've got to be very careful. We're being guided by the medical people here. At the moment he's not in position to return to training."
Hughes also expects to once again be without captain Ryan Shawcross (back) and fellow defender Bruno Martins Indi (groin) when he takes his team to Pep Guardiola's league leaders.
Jese Rodriguez, who missed the win over Southampton before the international break due to compassionate reasons, will return to the squad but Stephen Ireland is continuing his rehabilitation from the broken leg he suffered in May 2016.
Provisional Squad: Butland, Grant, Zouma, Wimmer, Johnson, Pieters, Souttar, Diouf, Tymon, Fletcher, Adam, Afellay, Jese, Shaqiri, Choupo-Moting, Sobhi, Berahino, Crouch.