Lee (1-0) didn't win his first game last year until July 4, but the former Cy Young Award winner outpitched Kris Medlen (0-1) with temperatures in the low 40s and a light mist falling most of the game.
Philadelphia scored two runs in the second on Ben Revere's fielder's choice RBI and Chase Utley's sacrifice fly RBI.
After Lee watched Cole Hamels and Roy Halladay lose the first two games by a combined 16-7 score, the left-hander walked none and struck out eight in 106 pitches to give the Phillies' renowned threesome a big lift.
Lee left for pinch-hitter Freddy Galvis in the ninth. Jonathan Papelbon earned his first save by striking out pinch-hitter Ramiro Pena, getting Andrelton Simmons to ground out and striking out Jason Heyward.
The Braves lost for the first time in 24 starts by Medlen, who beat the New York Mets last Sept. 30 to surpass the mark of 22 straight starts set by Carl Hubbell of the New York Giants in 1936-37 and matched by Whitey Ford of the New York Yankees in 1950 and '53.
Medlen, who allowed six hits, two runs, four walks and struck out three in five innings, labored through the first three innings on 61 pitches.
Lee, who either lost or received no-decision in his first 13 starts last season, improved to 4-1 with 0.77 ERA - a span of 47 innings in his last six starts against Braves.
Dan Uggla singled in the second and Justin Upton singled in the fourth off Lee, who did not allow a runner to get in scoring position.
Though he finished the outing with respectable numbers, Medlen hardly resembled the blossoming ace who went 9-0 with a 0.97 ERA in 12 starts last season and was named NL pitcher of the month in both August and September.
Medlen issued a walk to load the bases once in the first and twice in the second. He escaped the jam in the first, but wasn't so fortunate the next two times.
The Phillies, who were 1 for 11 with runners in scoring position on Wednesday, left the bases loaded in the first, but took their first lead of the series in the second.
After Lee drew a walk to load the bases with no outs, Laynce Nix scored on Ben Revere's fielder's choice RBI grounder to make it 1-0. Jimmy Rollins walked to reload the bases before Chase Utley's sacrifice fly RBI scored Erik Kratz for a 2-0 lead.
Lee had 15 no-decisions in 30 starts last season, tied for most in the majors with Cincinnati's Mat Latos, but against Atlanta, he extended his major league mark to 18 straight starts of pitching at least six innings and walking either none or one.
Since beating the Mets last July 4 in New York, Lee is 5-2 with a 1.61 ERA in 10 starts on the road
Cory Gearrin and Jordan Walden pitched the sixth and seventh for Atlanta. Anthony Varvaro pitched the eighth and ninth.