Gonzalez said Braves trainers explained a classic oblique injury is "not good."
Beachy lasted only two innings. He said he injured his side when he struck out swinging in the bottom of the second inning. He was pulled after making two warmup throws before the third inning.
"I felt a tearing sensation," Beachy said. "But not ever having had anything like this happen before, I'm not about to take myself out of the game without trying it. And I tried. I threw the first one and it hurt. But I tried to convince myself to push past that barrier. But it didn't."
If the injury is as severe as feared, Beachy would be placed on the disabled list, leaving the team looking for another No. 5 starter. Left-hander Mike Minor and right-hander Rodrigo Lopez are candidates to be recalled from Triple-A Gwinnett.
"I've got a really bitter tasted in my mouth," Beachy said.
Howard led off the eighth with a double to right. With one out, Ibanez singled to right. Joe Mather's throw beat Howard to the plate but short-hopped catcher Brian McCann, who couldn't hold on as Howard scored the go-ahead run.
Braves reliever Cristhian Martinez replaced Beachy and retired all 12 batters he faced.
Martinez had four strikeouts in four perfect innings. He delivered the surprise of the night when he drove in two runs with a double off Cole Hamels in the fifth for the first hit and RBIs of his career. The double, which drove in Alex Gonzalez and Mather, tied the game at 3.
"I'll tell you what, we really had no business being in this game after your starter goes two innings with an oblique," Fredi Gonzalez said. "Martinez, wow! Kept us in the ballgame and gave us a chance to get back in. He did everything he could."
Antonio Bastardo (2-0) struck out Freddie Freeman with the bases loaded to end the seventh.
Heyward didn't start for the third straight game due to inflammation in his right shoulder. He said he hopes to be able to start by Sunday.
With two outs in the sixth, Alex Gonzalez singled and moved to third on Mather's double. With pinch-hitter Diory Hernandez at the plate, Hamels threw a wild pitch, allowing Gonzalez to score for a 4-3 lead.
O'Flaherty and McCann began to leave the field on what they believed was a called third strike on Victorino, but umpire David Rackley called the pitch a ball. Victorino then tied it with his single to center, leaving McCann complaining to the umpire.
NOTES: Braves pitching coach Roger McDowell returned from his two-week suspension for making homophobic comments and crude gestures toward fans in San Francisco. ... Victorino has a 15-game hitting streak. ... Martinez was 0 for 8 in his career at the plate before his double. ... Prado was thrown out trying to steal second to end the third inning. The Braves are last in the major leagues with only six stolen bases — on 18 attempts. Prado has been caught on four of his five attempts.