Carroll, who came on as a second-half substitute at St Mary’s, received a kick to the back of his knee and left the stadium on crutches.
“The sad thing for us is the injury to Andy Carroll which we can ill-afford to take with our injury problems,” said Allardyce.
“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.”
Meanwhile, Allardyce says he intends to appeal the red card shown to goalkeeper Adrian after he was dismissed for handling the ball outside his penalty area.
“It was a foul on our goalkeeper before,” he said. “There is no doubt Mane had his hands on Adrian.
“Adrian made a mistake in the beginning but the linesman saw two hands on the ball but not the two hands on the back.
“We will be appealing it and I’ll be very disappointed if he doesn’t get off.”