Defending champion Schauffele sank a pressure-packed five-foot birdie at the last for a six-under-par 66 in the final round at Sheshan International.
McIlroy could only par the last after a poor drive, missing a 25-footer for the victory. He shot 68.
The pair finished at 19-under-par 269. (Reporting by Andrew Both in Tokyo; Editing by Simon Cameron-Moore)
Bradley Wiggins (Stage 20, 2012)