Brian McCann had four hits, including two homers. Freddie Freeman also homered for Atlanta.
It was the second extra-inning game in four days for the Reds, who lost 5-4 in 19 innings in Philadelphia on Wednesday night.
Carlos Fisher (0-2) walked Schafer to lead off the 12th. Fisher, working his second inning after throwing 5 2-3 innings in Wednesday night's game, also walked Martin Prado.
The switch-hitting Jones, batting from the left side against the right-handed Fisher, pulled a pitch past second baseman Brandon Phillips into right field. The speedy Schafer easily beat Jay Bruce's throw to the plate.
The teams combined for 30 hits.
Scott Linebrink (1-1) pitched two scoreless innings. He gave up a hit and issued an intentional walk in the 12th before ending the inning on Drew Stubbs' double-play grounder.
Stubbs had three hits and drove in three runs and Jonny Gomes had four hits for Cincinnati.
Arroyo gave up nine hits — including third-inning homers by McCann and Freeman — and five runs. He has given up 18 runs in 12 2-3 innings over his last three starts.
Arroyo was making his first start since an MRI showed a minor muscle strain in his back.
Lowe left the bases loaded in the first and third innings, retiring Bruce on infield grounders to end each Cincinnati threat.
Lowe's luck ran out in the fourth, when the right-hander blew a 5-0 lead. Stubbs had a three-run double over the head of right fielder Eric Hinske, followed by a run-scoring double by Phillips. Joey Votto's single to center drove in Phillips to tie the game.
Lowe, who walked five for the second straight start, gave up seven hits and five runs in 3 1-3 innings.
Left-hander Jeremy Horst, called up from Triple-A Louisville earlier in the day, had to wait only a few hours for his major league debut. Horst retired the Braves in order in the fourth and had a run-scoring single in his first at-bat in the fifth. He had four strikeouts in 2 2-3 innings and gave up only one run, McCann's second homer.
Schafer had Atlanta's top defensive play in the seventh when he made a running basket catch at the wall in left-center field to rob pinch-hitter Fred Lewis.
The Reds wasted a scoring chance in the eighth when Scott Rolen's single to left field off Jonny Venters moved Votto to third base, but Rolen was thrown out at second base by left fielder Martin Prado.
NOTES: RHP Daryl Thompson, who gave up five runs in three innings in his only appearance with Cincinnati, was optioned to Double-A Carolina. ... McCann had his seventh career two-homer game while matching his high with four hits. ... Gomes raised his batting average from .168 to .191.