The 48-year-old Perry dropped the putt on the third hole of a playoff against Charley Hoffman.
Perry shot a 2-under-par 69 and Hoffman had a 67 in the final round, tying at 14-under 270.
Kevin Na (68) was another shot back.
"To me this (TPC Scottsdale) is a place I always felt like I could win," Perry said after his $1 million victory. "I always felt very comfortable on this golf course ... ."
Hoffman was seeking his second win on the tour.