"They swing the bat, you know, and you make a mistake or put the ball over the plate and they hit the ball out of the ballpark," Braves manager Fredi Gonzalez said. "Today we didn't have enough runs where we could absorb that."
Donaldson belted a game-ending leadoff shot against Sugar Ray Marimon (0-1) for his third homer in two days. The drive into the second deck in left was Donaldson's third hit of the afternoon.
It was the second major league appearance for the 26-year-old Marimon, who pitched four innings in an 8-2 loss to Miami on Tuesday.
"We considered a lot of stuff, but that was our best option," Gonzalez said.
Danny Valencia went 4 for 4 for Toronto, and Bautista connected for his third homer. Valencia matched his career high for hits, accomplished three other times.
In the Blue Jays' 12th game of the season, particularly after losing three of four in the opening series at home against Tampa Bay, Toronto manager John Gibbons felt this kind of win was coming.
"We've had some opportunities this year at home to maybe make a run late, walk-off type thing," he said. "We've been in a position to do it, but just couldn't come through with it. So we definitely needed that."
Brett Cecil (1-1) picked up the victory after working a scoreless 10th.
It was Atlanta's first road loss of the season.
"I don't know what more we could have done from our side of the ball," Wood said. "I thought we played great baseball, played hard the whole game, hit, played defense, pitched well."
Wood allowed three runs and nine hits in 6 2-3 innings. The left-hander failed to record a strikeout for the first time in his career, but also induced four double plays.
"It's kind of weird," first baseman Freddie Freeman said. "I don't think he had a strikeout all game, but he kept the defense in it and that's what a pitcher's got to do, keep us in the game, and he definitely did that today."
Freeman and A.J. Pierzynski homered in back-to-back innings to help the Braves to a 4-0 lead.
Blue Jays: OF Michael Saunders (hamstring) was expected to resume his rehab assignment for Single-A Dunedin. Gibbons said the earliest he could rejoin the Blue Jays is next weekend in Tampa Bay.
Braves RH Shelby Miller (1-0) faces Daniel Norris (1-0) on Sunday. In his second career start in Toronto, Miller will be hoping to replicate last year's success, when he tossed a three-hit shutout as a member of the St. Louis Cardinals.
HAMMERING THE NL
The home runs for Bautista and Donaldson ran Toronto's total to 144 for interleague play. No other major league club has hit more in interleague games.