The Phillies trailed by a run heading into the ninth, but rallied against Rafael Betancourt (2-4).
Erik Kratz doubled to open the ninth and gave way to pinch-runner Casper Wells, who went to third on a groundout by John Mayberry. Pinch-hitter Carlos Ruiz doubled home Wells and Jimmy Rollins drew an intentional walk.
That brought up Young, who hit Betancourt's first pitch to left for the game-winning blow.
Jacob Diekman (1-3) benefited from the rally to pick up the second win of his major league career. He struck out two while working a perfect top of the ninth.
Nolan Arenado singled in a run for Colorado in the eighth to give the Rockies a 3-2 lead.