The Pirates won twice in the three-game series and have seven victories in their last nine contests.
Pittsburgh starter Charlie Morton gave up two runs on five hits with six strikeouts in six innings, but he was in position to be the losing pitcher when he left the game.
Instead, the Pittsburgh comeback gave the victory to Denny Bautista (1-0), who was recalled from Class AAA Indianapolis last weekend. Bautista threw two relief innings, striking out two, and Matt Capps worked the ninth for his 24th save.
Philadelphia starter J.A. Happ (10-3) went the distance. Happ gave up a leadoff single to Ronny Cedeno in the eighth, and then retired the next two batters before Jones hit his 15th homer of the season.
The other Pittsburgh run came on a first-inning home run by Andrew McCutchen.
Despite the loss, Philadelphia finished the day with a seven-game lead over Florida and Atlanta in the National League East.
Copyright 2009 by United Press International.
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