The decision kept the Orioles within a half game of the New York Yankees for the lead in the American League East. Baltimore also took over the best wild card record in the league by a half game over Oakland.
It had been a 1-1 game since the fourth inning when Nate McLouth singled with one out in the 11th off Josh Kinney (0-3), who has made 86 relief appearances in a career that began in 2006 and has only one win to show for it.
Jones followed McLouth to the plate and hit a 3-2 pitch over the wall in left.
That gave the win to Luis Ayala (5-4), who retired the final batter in the 10th inning. Jim Johnson worked the 11th inning and gave up two hits and a walk. He was helped out, however, by a double play and a caught stealing while picking up his 45th save.