Allardyce had agreed with England manager Roy Hodgson that the striker would not play the full game ahead of the upcoming World Cup qualifiers against San Marino on Friday 12 October and Poland on Tuesday 16 October.
But the West Ham manager was forced to leave the former Newcastle forward on because of West Ham's injury problems.
Carroll had a great chance to score when the game was level at 1-1 but he headed just wide and the Hammers boss believes the 90 minutes will benefit him.
He said: "Carroll is fine, I spoke to Roy Hodgson this week. We didn't want him to do 90 minutes today but because of the injuries we had to and it would have done him the world of good.
"It's a shame he didn't score, that one header dropped the wrong side of post. Hopefully he will be fit for a long time now and be an asset to us."
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