Carroll ruled out for at least three weeks
The England forward came off the bench early in the second half at St Mary's Stadium and remained on the field despite suffering the problem.
Despite having goalkeeper Adrian sent off for handling the ball outside his area, West Ham held on for a 0-0 draw that leaves them eighth in the Premier League.
Carroll was later seen leaving the stadium on crutches and Allardyce has confirmed it is a recurrence of a previous problem.
"The sad thing for us is the injury to Andy Carroll which we can ill-afford to take with our injury problems," he said.
"It's the same knee. He got kicked on the back of it and felt something was wrong. He stayed up and was a nuisance but I just hope that staying on hasn't done any damage.
"He got fit in two-and-a-half weeks but clearly it's going to take longer this time because it's the same injury."