The Welsh, already rocked by injuries to key backs Leigh Halfpenny and Rhys Webb in their final warm-up match, had six players added to their casualty list during Sunday's 54-9 victory in Cardiff.
Allen pulled up with the injury in the second half and after having scans was replaced in the squad by Tyler Morgan, who joins Scott Williams and Jamie Roberts to restore the number of specialist centres in the squad to three.
British and Irish Lions centre Jonathan Davies was ruled out of the tournament by a knee injury.
Wales next face England in a Twickenham clash on Saturday which could go a long way to deciding which teams progress from Pool A, which also includes Australia and Fiji.
"It's disappointing to lose Cory in this way, especially following his man-of-the-match display against Uruguay," said Wales coach Warren Gatland. "Tyler was part of the our extended squad and trained very well and will link up with us in London later today."
The other injured players were fullback Liam Williams (dead leg), props Paul James and Samson Lee (tight calves) and their fellow front-rower Aaron Jarvis (rib cartilage).
Flanker Dan Lydiate was, however, given the all-clear after a head knock.
With only two fully fit props in his squad, Gatland will have to make a call this week on whether the injured players have recovered sufficiently or need to be replaced.
Once players have been replaced in the squad, however, they can play no further part in the tournament.
Gatland knows that a match against England at Twickenham is not a place for players nursing injuries.
"It’s going to be a tough battle up front, that’s what I’m expecting," the New Zealander said after the Uruguay match.
"We’ve got to go out there and be expressive and be prepared to move the ball if we need to. But we’ve to be combative up front and try and negate some of the English strengths."
(Reporting by Nick Mulvenney, editing by Ed Osmond)
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