Fitzpatrick was placed third after opening rounds of 68 67, but a level-par 72 on Saturday followed by a one-under 71 in the final round foiled his tilt at the title at the Amata Spring Country Club.
His reward for tieing for 11th place with amateur Jin Cheng, of China, was around £11,500.
Donaldson, who had led after the first two rounds but went into the final day two shots adrift of France's Clement Sordet, closed with a seven-under-par 65 to add to his earlier scores of 63 68 71.
He beat both the Frenchman Sordet (71 66 63 70) and Worksop's Lee Westwood (71 68 64 67) by three to earn almost £120,000.
Fitzpatrick began the day by birdieing the first hole for the third time in four rounds, but gave the shot back quickly at the fifth.
His back nine started with a bogey, but he birdied both the 12th and the 18th, narrowly missing an 11th top-10 finish in his first full year as a tournament professional.