Brazilian striker Amoroso opened the scoring for Sao Paulo after quarter of an hour before the Saudis equalised through Noor to leave the game all square at half time.
Amoroso scored his second two minutes into the second half and Sao Paulo opened up a two goal lead just before the hour mark when goalkeeper Ceni converted a penalty.
Al Montashari pulled a goal back for the Saudis but Sao Paulo held on for the win and will meet either Deportivo Saprissa or Liverpool in the final on Sunday.