Happ (10-3), who lost for the first time in four decisions, appeared to be cruising following McCutchen's drive into the center field shrubbery leading off the first. The left-hander allowed only four more hits over the next six innings and only once pitched with multiple runners on base.
After pinch-hitter Ronny Cedeno singled to start the eighth, Happ - who threw 114 pitches - quickly got the next two batters on fly balls. But Jones, who leads NL rookies with 15 homers, drove a 1-1 pitch over the center-field wall to give the Pirates the lead and prevent Happ from becoming the first Phillies rookie to win 11 games in a season since Bob Walk in 1980.
Jones has been quite a find for the Pirates after being cast off by the Twins, hitting .291 while anchoring the middle of the order following the trades of Nate McLouth, Adam LaRoche and Freddy Sanchez.
The Phillies still own a seven-game lead in the NL East, but they won only one of three in cross-state Pittsburgh and needed Ryan Howard's three-run homer in the 10th inning to do that Wednesday, winning 4-1.
Capps had two terrible outings earlier against the Phillies, allowing five runs in one-third of an inning to lose 8-7 on July 11 and two runs in the ninth to blow a save Tuesday, although the Pirates came back to win 6-4 on McCutchen's two-run homer in the bottom of the inning. Capps allowed one hit while converting his 24th save in 28 opportunities.
The Pirates had rallied in the ninth each of the previous two games against the Phillies' shaky bullpen, but this time did it against one of their starters.
McCutchen's homer, his ninth, tied it at 1 after Morton managed to limit Philadelphia to one run on Ryan Howard's RBI grounder in the top of the inning despite allowing the first four batters to reach base. Paul Bako's second homer of the season made it 2-1 in the second.
Morton gave up five hits and two runs in six innings, striking out six.
As during the first two games of the series, there was a large number of Phillies fans mixed in with Pirates rooters in the crowd of 24,470. In the eighth, Chase Utley's long drive to left field generated a noisy reaction from Phillies' fans, but there were even louder cheers when Lastings Milledge caught the ball on the warning track.
NOTES: Phillies SS Jimmy Rollins ranged far to his left to make a diving stop behind second base of Morton's grounder in the fifth and threw out the pitcher by a step. ... At least one home run was hit in the first inning in all three games. Rollins led off Tuesday's game with a homer, and Utley went deep on Wednesday. ... The Pirates went 7-2 on a nine-game homestand against the Brewers, Reds and Phillies that began with five consecutive victories.