Craig Kimbrel gave up a leadoff single to Roger Bernadina and walked Zack Cozart to open the ninth. Kimbrel struck out Brayan Pena and Chris Heisey before earning his seventh save on Joey Votto's groundout.
First baseman Freddie Freeman made a long stretch for Chris Johnson's throw from third base on Heisey's groundball. Reds manager Bryan Price challenged first base umpire Vic Carapazza's ruling that Freeman's foot remained on the bag. The call was confirmed, ending the game.
Two Cincinnati players left the game with injuries. Third baseman Todd Frazier was pulled in the fifth with tightness in his left leg. Catcher Devin Mesoraco strained his left hamstring and stumbled after rounding third base in the seventh, before limping across home plate.
Santana (3-0) led 5-0 through five innings before allowing two runs in the sixth and two more in the seventh. He gave up four runs on nine hits in 6 2-3 innings.
In 2013, Justin Upton led the majors with 12 homers in April, becoming the fastest player in Braves franchise history to reach the mark. He has hit 35 homers in April for his career, his highest total for any month.
Freeman had three hits for Atlanta.
B.J. Upton, who was hitting .205, had one hit in his first game wearing prescription glasses.
Bailey allowed five runs on nine hits in six innings. He allowed at least four earned runs for the fourth time in five starts this season and has a 6.15 ERA.
The Braves increased their lead to 4-0 in the second. Andrelton Simmons doubled and scored on Heyward's two-out single. In the third, Freeman singled, moved to second on a wild pitch, advanced to third on Justin Upton's deep fly ball to centerfield and scored on a single by Evan Gattis.
Trailing 5-0, the Reds scored two runs in the sixth. With runners on second and third following Votto's walk and Brandon Phillips' double, Jay Bruce had a run-scoring single. Phillips scored when Neftali Soto hit into a double play.
A strong defensive play by right fielder Jason Heyward helped Santana in the first inning.
Votto doubled with one out in the first and moved to third on Phillips' bloop single. Votto was thrown out at the plate on a strong throw by Heyward on Jay Bruce's fly ball. Votto, sliding head-first, was tagged out in the batter's box and never reached the plate.
NOTES: Price said closer Aroldis Chapman, recovering from facial fractures and a mild concussion when hit by a line drive on March 19, will throw 35 to 40 pitches in batting practice on Saturday. If it goes well, it should be Chapman's final test before he is cleared for a minor league rehab assignment. ... Braves RHP David Hale will look for his first win of the season when he faces Reds RHP Mike Leake on Saturday.