Nolan sustained the injury in training on Thursday and played no part in the club's 3-1 win at Crystal Palace two days later.
And manager Allardyce has now revealed that Nolan is not likely to return until October, in a "massive blow" for the club.
But Allardyce hopes that their excellent win at Selhurst Park shows they can find a way without their skipper, who has scored 17 goals in 69 top-flight appearances for West Ham.
Allardyce said: "Kevin fractured his shoulder and that's a massive blow to us, along with all the other players we've got injured.
"He will be out for probably six weeks I would think.
"It isn't a dislocated shoulder, it's a fractured shoulder, but I don't know just how long that will keep Kevin out.
"We dealt with it brilliantly at Palace and let's hope we can continue to do that. It didn't affect us at Palace and maybe that's a sign there's more to come."
Mark Noble will deputise as West Ham skipper in Nolan's absence.
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