Alpha, the 7-1 longshot, took the lead out of the gate and went on to capture Saturday's 60th running of the $750,000 Woodward Stakes at Saratoga Race Course.
Trained by Kiaran McLaughlin and ridden by John Velazquez, Alpha found the winner's circle for the first time this year and the first since last year's Travers Stakes.
"It's great, one of the biggest wins of our career I think," McLaughlin said after the race.
Alpha, owned by Godolphin Racing, broke first out of the gate as 3-2 favorite Paynter got off to slow start. Alpha led the five-horse field around the first turn and into the backstretch while racing off the rail on the sloppy track.
Racing second was Flat Out with Paynter to his inside followed by Successful Dan and Ron the Greek. Early scratches were Fort Larned with an injury and Mucho Macho Man, who was held out because of the sloppy track.
Around the final turn, Flat Out and jockey Junior Alvarado began to move closer to Alpha and drew even with the 4-year-old colt coming into stretch. Flat Out was in the middle of the track outside of the leader.
Flat Out moved toward Alpha as the pair drove through the stretch, but Velazquez was able to guide his mount to a head victory over the 7-year-old veteran.
"Well, I talked to John and said if he breaks well and you can clear Paynter, let's go. It worked in the Jim Dandy," McLaughlin said. "Maybe I didn't have him fit enough the first two races here, but he loves it here."
Successful Dan finished third followed by Ron the Greek and Paynter.
Alpha covered the 1 1/8 miles in 1:49.28 on the sloppy surface.
Alpha notched a win after four earlier losses this year. He had two starts in Dubai and came back to New York where he finished fourth to Flat Out in the Suburban Handicap and sixth in the Whitney Invitational.
The colt adds $450,000 to his earnings which now total $1,772,500 with six wins in 16 career starts.
His last win came in last year's Travers when he dead heated with Golden Ticket. He had gone six starts between wins.
Alpha returned $17.40, $6.30 and $3.40. Flat Out paid $3.50 and $2.20, and Successful Dan paid $2.80 to show.