Casey Kotchman had a two-run double and Kelly Johnson added his fourth home run for the Braves, who have won the past two nights without injured Chipper Jones. They also played without injured shortstop Yunel Escobar on Saturday.
The Braves will go for a series sweep Sunday afternoon against Toronto in the finale of an eight-game homestand. They have won four of their past five home games, after losing 11 of the previous 14.
Meanwhile, the American League East-leading Blue Jays are mired in a season-high five-game losing skid.
"We needed to start playing better at home, that's the most important thing," said Lowe (6-2), who induced 16 groundball outs and notched his fifth win in six starts. "It starts with starting pitching. You've got to be able to keep your team in the games, and we've been able to do that."
Braves starters have the third-best ERA (3.81) in the NL, after finishing with a 4.60 ERA in 2008 that ranked 11th in the league.
Johnson's seventh-inning solo homer — his fourth of the year and first since April 14 — increased the lead to 4-2, a cushion that proved crucial after the Blue Jays got to Gonzalez in the ninth.
"That's the most important part, that it ended up being the difference," Johnson said. "It was good that we got enough runs for Derek. It's ridiculous how good the guy's been all year."
The Blue Jays got two hits and two walks in the ninth against Gonzalez, who recorded one out before he was replaced by Soriano.
"Soriano did an unbelievable job," Lowe said. "That's the benefit of having two guys who are comfortable closing."
Marco Scutaro's two-run double in the third inning gave the Blue Jays an early lead, but the Braves answered with two in the bottom of the inning on singles by Lowe and Johnson, and Kotchman's double off the center-field wall.
An inning later, Jeff Francoeur doubled to left field, his second hit of the night. Rookie shortstop Diory Hernandez, in his first major league start, drew a walk before Jordan Schafer grounded out to advance both runners.
Blue Jays starter Casey Janssen (0-1), in his first major league game since 2007, probably figured he'd get out of the inning with Lowe coming to bat.
But the 35-year-old pitcher lined a ball through the right side to drive in Francoeur for a 3-2 lead. Lowe entered the game with a .125 career batting average, though he had a pair of two-hit games last season for the Dodgers.
Johnson's homer was just the eighth by the Braves in 22 home games this season, easily the fewest in the majors.