Allen suffered the injury on the stroke of half time as the Potters recorded an emphatic 5-1 win, but the former Swansea City midfielder will now miss the rest of the season.
“He’s ruptured his Achilles, he had to be helped off at half-time,” Stoke boss Michael O’Neill told BBC Radio Stoke after the game.
“You fear the worst, you hope for the player it is not the case, but the news is not what we hoped for and he will need surgery this week. The club will do everything they can to look after him and make sure he’s back as soon as possible.
“It’s a huge loss, he’s a terrific player and a terrific lad. I am gutted for him, he had so much to look forward to with Euro 2020 as well.
“Our thoughts go with him, but obviously the club will do everything they can to look after him and make sure he’s back as soon as possible.”
Allen was instrumental as Wales qualified for their first ever European Championships in 2016 and the former Liverpool midfielder was named in the team of the tournament as The Dragons reached the semi-finals before being eliminated by eventual champions Portugal.
Wales have been drawn against Italy, Switzerland and Turkey in Group A for EURO 2020, which runs from June 12 to July 12.
