Chris Davis drew a leadoff walk from B.J. Rosenberg (0-1) in the 12th and Jones followed by slamming a pitch into the bullpen in left-center field, boosting the Orioles to their eighth extra-inning victory of the year.
The long ball was the 17th of the season for Jones, whose blast allowed Baltimore to even its three-game series at Camden Yards.
Luis Ayala (2-1) was credited with the win after setting down the Phillies in the top of the 12th.
Philadelphia forced the extra frames on an RBI single by Jim Thome in the eighth inning. Thome also cracked a solo homer -- his 605th career shot and first of the season.
Vance Worley held the O's to three runs (one earned) on five hits in a six-inning start for Philadelphia.
Hunter Pence went 4-for-5, while Hector Luna added a solo homer for the losers.
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