The Texan, team mate to championship leader Jorge Lorenzo, suffered a shoulder separation, a cracked rib in his upper chest area and bruising to the lung after falling in the wet race at Sepang.
Spies, who is joining Pramac Ducati next season, will make a full recovery although he will need to remain in a sling for up to 10-12 weeks.
Spies is 10th in the championship with just 88 points to Lorenzo's 330.
The decision on a replacement rider for the final round of the Championship at Valencia will be clarified by Yamaha following the Phillip Island weekend.
