Freddie Freeman, Martin Prado, Heyward and David Ross all connected off Phil Hughes (7-6) to build a 6-1 lead on a sticky, 94-degree afternoon. Michael Bourn stole what might've been another home run from Jayson Nix after missing an earlier opportunity for a try at a leaping grab.
Alex Rodriguez hit his 640th career homer, and Robinson Cano, Derek Jeter and Eric Chavez all hit long balls against Tommy Hanson (8-4).
"It's just that kind of ballpark," Heyward said, "but at the same time we got two teams that are capable of hitting some home runs."
The Yankees, who have a major league-leading 105 homers, managed just four other hits in their second straight loss after a 10-game winning streak. They pulled to 6-5 on Curtis Granderson's RBI single in the seventh but Rodriguez ended the inning with a double-play grounder.
"It's been up and down, like a lot of our other hitters," manager Joe Girardi said of Rodriguez's season.
In the eighth, Freeman hit an RBI single and Heyward a two-run shot off Boone Logan to help Atlanta pull away for its third win in 10 games and second straight against New York. The Yankees swept the Braves in Atlanta last week.
Heyward had the go-ahead hit Tuesday night and added a triple.
"We're really, really good when Jason's swinging the bat well."
Even though he didn't start in a day game after playing Tuesday night, Chipper Jones still was a factor early. In the final year of a Hall of Fame-worthy career, Jones was honored before his last regular-season game against the Yankees. On behalf of the Yankees, Jeter and former Braves teammate Andruw Jones gave Chipper third base from Tuesday's game. In 19 years with Atlanta, Chipper Jones faced the Yankees in two World Series.
With the sun beating down on the crowd of 45,094, the public address announcer urged fans visit the cooling stations set up in the concourses.
Girardi emphasized how important it was to be aggressive early on a day that felt as if it were over 100 degrees with the oppressive humidity. The Braves were.
Bourn singled leading off and, with two outs, stole second without a throw. He scored on Dan Uggla's single to left. Freeman wasted no time, connecting on the first pitch he saw for a two-run drive into the New York bullpen in right-center to make it 3-0.
Jeter got one back with his fourth leadoff homer of the season, hitting Hanson's first pitch into the stands in right-center.
"When Jeter caught that one in the first, I was like `here we go,'" Ross said.
Hanson only gave up one hit after Jeter's homer until Chavez led off the fifth with a drive to straightaway center field. Bourn watched the homer clear the fence and land in the netting over Monument Park then jumped and smacked his hand to glove.
Bourn made the play he wanted after a walk to Russell Martin, ranging far to his right to snare Nix's fly above the wall to protect a 6-2 lead.
Heyward stood at the fence in right field and watched Rodriguez's high fly leading off the sixth carry into the stands. The RBI was A-Rod's 1,925th, breaking a tie with Jimmie Foxx for sole possession of sixth on the career list.
Cano followed with a smash deep into the stands in right-center to end Hanson's day for the Yankees' third back-to-back homers of the season -- one was three in a row.
Hanson matched a career high with the four homers allowed. He came in 6-0 with a 1.22 ERA against AL East teams, but gave up four runs in five-plus innings this time.
All season Hughes has been hurt by the homer, giving up at least one in each of his first 12 starts before keeping the ball in the park in his previous outing. The career-most four allowed Wednesday boosted his total to a majors-leading 19 this year.
"He just didn't have great location today," Girardi said.
NOTES: Teams have combined to hit eight homers at the ballpark that opened in 2009 three times. ... Mark Teixeira was out of the Yankees lineup Wednesday. He was hit on the left foot by Heyward's hard grounder Tuesday night and Girardi said the first baseman was still sore. He doubled as a pinch-hitter in the eighth. ... Former Yankees center fielder Bernie Williams was chosen as manager of the World Team in the All-Star weekend Futures Game for minor leaguers on Sunday, July 8 in Kansas City. ... The 94 degrees at game time was not the hottest start for Atlanta. It was 97 degrees in Arizona when they faced the Diamondbacks on April 21 with the roof open. ... The Yankees are the last team to allow 10 runs in a game. ... Heyward has three multihomer games.