"He's really done great. Obviously, he's the catalyst," reliever Javier Lopez said of Pagan. "Everybody's stepped up in Melky's absence. It's a new era every night."
Pablo Sandoval hit an RBI double and scored the tying run for the National League West-leading Giants on a wild pitch in the third, and Buster Posey doubled in a run after missing the previous two games with tightness in his right hamstring.
Freddie Freeman hit two solo home runs for his third career multihomer game, and Jason Heyward also connected for the Braves, who lost for the sixth time in seven games. Freeman hit his 16th and 17th homers of the year. He connected twice at Arizona on April 19.
"Pagan caused a wreck out there," Freeman said. "We couldn't get him off the bases. He really changed the game for them."
Vogelsong (11-7) won despite allowing his 11th, 12th and 13th homers of the year -- his most since surrendering three homers to the Cubs on April 20, 2004, while with Pittsburgh.
The right-hander and surprise 2011 All-Star, who dropped out of the NL ERA lead with his recent struggles, ended a two-start skid in which he didn't make it past three innings either outing, a 14-2 home loss to the Nationals on Aug. 13 in which he went 2 2/3 innings and then a 7-1 defeat Sunday at San Diego after being knocked out after three innings.
He picked up a couple of things off video to get better direction to the plate with his pitches and was encouraged by his progress despite the three homers.
"They're both strong guys, and if they barrel it, it's going to go a long way," he said. "I'm just glad they were all solo shots."
San Francisco (71-55) moved a season-best 16 games over .500, one shy of matching the club's best mark of 17-over last year.
The Giants maintained a three-game lead over the Dodgers in the division -- their largest since July 26 -- and they haven't held a four-game cushion since leading Arizona on July 29, 2011. Los Angeles beat the Marlins 11-4 at home.
Pagan finished 4-for-5 and is batting .450 (18-for-40) over his past nine games since the Giants lost Cabrera to a 50-game suspension for testosterone Aug. 15.
"He's been amazing," Vogelsong said. "It's been fun to watch."
After Freeman hit his 15th home run leading off the second, Vogelsong retired the next 10 Braves in order.
Marco Scutaro had an RBI single for the Giants, who handed Braves starter Ben Sheets (4-4) his third loss in as many starts and fourth in five since a three-start winning streak. He was knocked out after a season-low 4 1/3 innings, tagged for four runs and nine hits with three walks and two strikeouts.
Sheets has allowed 14 earned runs over his past 16 1/3 innings.
"The scary thing was a lot of them were located pretty good," he said.
Sheets' third-inning wild pitch skipped off catcher Brian McCann's chest protector toward the first-base dugout. McCann retrieved the ball and threw to Sheets covering home, but Sandoval had already scored and the pitcher dropped the ball.
Sheets couldn't hold an early 2-0 lead after Heyward's first-inning home run and then Freeman's first clout of the game leading off the second.
Freeman and Heyward were the lone bright spots for the struggling Braves offense a night after they went 1-for-12 with runners in scoring position -- and were just 17-for-98 over their previous 12 games for the second-worst mark in the majors during that span.
"It's getting frustrating, honestly," Freeman said. "We're a winning team and we're just not winning right now."
Javier Lopez, the fourth Giants reliever, finished for his fourth save.
Vogelsong faced the Braves for only the third time in his career and second as a starter. He had a no-decision at Turner Field on July 18 despite allowing only one run and four hits in six innings before the Giants won 9-4 in 11 innings. ... Francisco Peguero, called up Thursday from Triple-A Fresno, is slated to make his major league debut starting in left field Saturday for the Giants. ... LHP Madison Bumgarner goes for his 15th victory Saturday against fellow lefty Mike Minor (6-10) while seeking his first career win versus Atlanta after an 0-2 record in his first three appearances. ... A decision on Aubrey Huff's status -- out since Aug. 1 with a right knee sprain -- is still "in a holding pattern," according to manager Bruce Bochy. ... Giants RHP Brad Penny (shoulder) allowed one unearned run and two hits in one inning of a rehab start for Class A San Jose on Friday night. Penny is eligible to come off the DL on Wednesday. ... The Giants haven't decided whether RHP reliever Guillermo Mota will rejoin the team right away when he is eligible to return from his 100-game suspension Tuesday. ... Vogelsong has given up two or more home runs only nine times in his career. This marked only the second time this year Giants pitchers gave up three homers at home.