ATLANTA — Braves manager Fredi Gonzalez was looking for a small sign of encouragement after his team's 90th loss.
That glimpse of encouragement came with rookie pitcher Matt Wisler avoiding an early knockout.
Wisler made it through six innings but gave up two homers in Toronto's four-run fourth as Atlanta fell 5-0 to the Blue Jays on Thursday night.
It was Atlanta's 15th shutout loss. Only San Diego, with 19, has more.
The Blue Jays lead the New York Yankees, who did not play Thursday, by 3 ½ games in the AL East. Toronto won two of three games for their first series win over the Braves since 2008.
Wisler (5-8) allowed four runs and nine hits in six innings. He has lost seven straight decisions since a 5-1 start, but he recorded two scoreless innings after the rough fourth.
"That was a big goal," Gonzalez said. "And we pushed him a little bit. We wanted him to go back out there. We gave him that challenge."
Marco Estrada (13-8) combined with Roberto Osuna on a three-hitter.
Cliff Pennington hit a three-run homer in the fourth. Edwin Encarnacion and Josh Donaldson also hit home runs.
Pennington's homer came on a 0-2 pitch.
"That can't really happen," Wisler said. "Two guys on base, I'm up in the count, I've got to make a better pitch to get out."
Estrada allowed three hits with four strikeouts and two walks in eight innings. He did not allow a baserunner to reach second base.
"He shut them down; he's been doing it all year," Blue Jays manager John Gibbons said.
Atlanta's first hit came in the third, a sharp grounder by Wisler that hit Estrada's right foot and bounced into left field. Cameron Maybin hit a grounder between shortstop and third base in the fifth for the second hit. With two outs in the eighth, Andrelton Simmons hit a line-drive single to right.
Encarnacion led off the fourth with his 33rd homer, into the fifth row of the seats in left field. Pennington hit a three-run shot later in the inning.
Donaldson added a ninth-inning homer off Sugar Ray Marimon.
The Braves finished 6-14 in interleague games. They have lost eight of their last nine series, including five straight at Turner Field.
They are 3-13 in September and have lost 26 of 30 and 41 of 53.
At 57-90, the Braves must win six of their last 15 to avoid a 100-loss season.
Former President Jimmy Carter and wife, Rosalynn, sat in their usual seats near the Braves' dugout. Carter, 90, recently announced he has cancer that spread to his brain. The two received a loud cheer when shown on the video board during the "Kiss Cam" promotion. Carter kissed his wife and then gave a big smile as the cheers continued.
BLUE JAYS: Gibbons said SS Troy Tulowitzki will join the team in Toronto after having a specialist examine his injured left shoulder. He was expected to miss at least two weeks after cracking his shoulder blade in a collision on Sept. 12.
BRAVES: LHP Manny Banuelos is expected to be ready for spring training after surgery Thursday to remove bone spurs from his left elbow.
BLUE JAYS: RHP Marcus Stroman will make his second start of the season Friday night in the opening game of a home series against Boston.
BRAVES: In the opening game of a series which could decide last place in the NL East, RHP Williams Perez will face Phillies LHP Adam Morgan on Friday night.