Ryan Howard started Philadelphia's winning rally with a leadoff single against Edwin Moreno, and Ibanez followed by hitting a 2-0 pitch into the right-field stands.
Padres manager Bud Black had to use Moreno (0-1) in the ninth because closer Heath Bell had worked three consecutive days. Moreno had not allowed an earned run in his first six appearances this season.
Ibanez, who signed a free-agent deal with the Phillies in the offseason, has four career game-ending homers. He finished 2-for-4.
Slumping shortstop Jimmy Rollins connected for a pinch-hit solo drive in the eighth for Philadelphia, which ended a three-game skid.
Clay Condrey (2-0) picked up the win working one inning in relief.
San Diego scored three times in the third inning against Chan Ho Park. Jody Gerut singled in Everth Cabrera to give the Padres a 1-0 lead, and Edgar Gonzalez followed with a sinking liner to left that Ibanez struggled with before it glanced off his glove for a triple. Brian Giles added a run-scoring groundout.
The Phillies got their first two runs in the sixth on Chase Utley's two-run shot.
Notes:@ The Padres placed RHP Walter Silva on the 15-day disabled list, retroactive to Tuesday, with a strained right forearm. ... SS Rollins and OF Jayson Werth were held out the starting lineup for the first time this season. Rollins opened the season just 6-for-45 over 10 games. Werth entered in a 3-for-17 slump over the last four games. ... Cabrera left in the sixth with a hand injury.
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