A mistake by keeper Jacob Spoonley allowed Sanfrecce to take the lead in the eighth minute, spilling a shot from Gakuto Notsuda that Minagawa turned into the net.
Sanfrecce were content to play on the counter-attack after that but doubled their lead with 20 minutes remaining when Brazilian substitute Douglas found Shiotani and his deflected shot beat Spoonley.
Club America of Mexico meet China's Guangzhou Evergrande in another quarter-final on Sunday, with the winners going up against European champions Barcelona.
Sanfrecce and TP Mazembe face off for the right to play Libertadores Cup champions River Plate of Argentina.
Barcelona and River Plate are directly through to the semi-final stage.
(Reporting by Martyn Herman; Editing by Tony Jimenez)
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