The seesaw game saw the Braves rally from a 6-0 deficit against Roy Halladay, then come back from four runs down in the eighth.
Dan Uggla led off the Atlanta 11th with a single. Jones just missed a homer on a ball that landed barely foul to right, then connected against Brian Sanches (0-1).
Jones' homer ended the Braves' eight-game losing streak to the Phillies.
Brian McCann hit a grand slam for Atlanta. Befitting a crazy game, he was poked in the eye with an errant high-five from teammate Michael Bourn after the homer.
It was the highest-scoring extra-inning game in the majors since Cleveland beat Kansas City 15-13 in 10 innings in 2006, STATS LLC said.
Ruiz had three hits, including a three-run homer in the seventh and a three-run double in the eighth. He was the first Phillies hitter to drive in seven runs since Ryan Howard against the Yankees on June 20, 2006.
Laynce Nix also hit a three-run double for the Phillies.
Braves closer Craig Kimbrel couldn't hold a 13-12 lead in the ninth. Shane Victorino's two-out infield hit drove in Juan Pierre, who walked and stole second and took third on a grounder.
Halladay had his worst start in five years. He gave up 12 hits - one below his career high - and eight runs in 5 1-3 innings.
Halladay was tagged by McCann's fifth career slam in the fifth. The former Cy Young winner had not allowed as many earned runs since May 5, 2007, when he gave up nine runs in 5 1-3 innings at Texas.
Martin Prado had three hits and drove in three runs, including a two-run single in the Atlanta eighth.
Braves reliever Eric O'Flaherty blew an 8-6 lead before recording an out in the seventh. Ty Wigginton walked, pinch-hitter John Mayberry Jr. singled and Ruiz followed with his fourth homer to left for a 9-8 edge.
Atlanta's Tommy Hanson gave up eight hits and four runs in 3 2-3 innings. It was his shortest start since he pitched 3 1-3 innings against the Mets on Aug. 6, 2011, in his last outing before he was placed on the disabled list for the remainder of the season with right shoulder tendinitis.
NOTES: Phillies LHP Cliff Lee, on the 15-day disabled list with a strained left oblique muscle, threw in the bullpen before the game. If he has no discomfort, he plans another bullpen session on Saturday. If all goes well on Saturday, Lee is expected to come off the disabled list. ... Atlanta's Jason Heyward missed his third straight start with soreness around his right oblique muscle before entering the game as a pinch-hitter and remaining in right field. ... The Phillies placed 1B Jim Thome on the 15-day disabled list with tightness in his lower back and recalled C Erik Kratz from Triple-A Lehigh Valley. The move was made retroactive to Sunday. ... The three-game series ends on Thursday when Braves RHP Randall Delgado (2-2) starts against RHP Joe Blanton (2-3).