Juanjo Cobo and Sergio Pardilla will take their places in the final monument of the European cycling sesason.
Valverde showed signs of fever on Wednesday which had increased by Friday, meaning he did not even travel to Italy.
Amador suffered his injury during Thursday's Gran Piemonte.
Meanwhile Sep Vanmarcke has also fractured his collarbone to drop out of the Circuit Franco-Belge and bring his own season to an end.
He is yet to sign with a team for 2013, having announced that he will leave Garmin-Sharp.
He won the Belgian semi-Classic Omloop Het Nieuwsblad ahead of Tom Boonen and Juan Antonio Flecha this year.