The Cubs built a 5-0 lead through five innings but the Phillies started the comeback with a four-run sixth and tied the score with Kevin Frandsen's home run in the seventh.
Bernadina was hit by a pitch by Kevin Gregg (2-4) and then stole second base. After a flyout, Young blooped a single to right and Bernadina beat the throw from right fielder Nate Schierholtz to score the game-winner.
B.J. Rosenberg (1-0), who pitched a one-hit eighth, collected the win and Jonathan Papelbon worked a 1-2-3 ninth for his 23rd save.
All the runs before the ninth came off Philadelphia starter Roy Halladay, who gave up five runs on seven hits and two walks in five innings, in his second start since early May.
Chicago's Jeff Samardzija left the game after 6 2/3 innings. He was charged with five runs on eight hits and two walks.
Anthony Rizzo gave the Cubs a 1-0 lead in the first with his 21st home run of the season. Schierholtz hit his 20th homer of 2013 and Starlin Castro added a two-run double in the fourth and Brian Bogusevic singled in Rizzo in the fifth, making the score 5-0.
Frandsen tripled and scored on Young's sixth-inning single ahead of a two-run triple by Chase Utley. Domonic Brown got Utley home on a groundout, pulling the Phillies within 5-4. Frandsen's fourth home run of the season tied the score in the seventh.