Medlen allowed only five baserunners and erased two of them on pickoffs at first base. He struck out nine to tie his career high and walked none.
Atlanta, the NL wild-card leader, ended the Padres' season-high eight-game winning streak.
Medlen (6-1) has not allowed a run since the second inning of a 9-3 victory against the New York Mets on Aug. 11. Five days after that, he threw his first complete game and shutout in a 6-0 victory against San Diego at Atlanta, allowing only five hits.
Atlanta has won Medlen's last 17 starts dating to May 2010 and is 20-4 in his 24 career starts.
Craig Kimbrel pitched the ninth for his 32nd save in 34 chances.
Dan Uggla homered to left leading off the fifth, his 1,000th career hit, and Chipper Jones hit an RBI double in the first, both off Andrew Werner, who was making his second big league start.
Werner (1-1) allowed two runs and four hits in six innings, struck out seven and walked none.
NOTES: A group that includes the sons and nephews of former Dodgers owner Peter O'Malley has closed its $800 million deal to buy the San Diego Padres. The team scheduled a news conference for Wednesday morning to introduce the new owners. The sale was approved by major league owners on Aug. 16. The new ownership group includes O'Malley's sons, Kevin and Brian O'Malley, and nephews Peter and Tom Seidler. Golfer Phil Mickelson, a San Diegan, also is involved with the group. He won't be at the news conference, though, as he's en route to the Deutsche Bank Championship outside of Boston. ... The series concludes Wednesday afternoon when RHP Tommy Hanson (12-6, 4.40) is scheduled to start for Atlanta against LHP Eric Stults (4-2, 2.68)