Medlen and closer Craig Kimbrel combined on the shutout.
Johnson's homer to left field snapped a streak of 16 consecutive batters retired by Lee, who allowed only three hits with no walks and 13 strikeouts in eight innings.
Medlen (15-12) strengthened his case to be the Braves' Game 1 starter in the NL division series next week. He allowed two hits with two walks and seven strikeouts. He has won five straight decisions.
Kimbrel pitched a perfect ninth for his 50th save.
Lee (14-8) completed a strong September finish despite the loss. He was 3-2 in five starts in which he had 54 strikeouts with only one walk.
The Phillies didn't have a hit through 5 2-3 innings before Cesar Hernandez beat out a grounder to third base for an infield hit. Hernandez was thrown out by Evan Gattis trying to steal second base. Chase Utley, who had Philadelphia's second hit on a seventh-inning single, was thrown out on a double-play grounder by Carlos Ruiz, leaving Medlen as having faced only one batter above the minimum.
Medlen walked Ruiz to lead off the second before Domonic Brown hit into a double play.
Lee struck out the side in the fourth and fifth innings as part of a stretch in which he retired 16 consecutive batters.
Reed Johnson, making his first start since July 25, made a running catch of Jimmy Rollins' liner in left field in the first inning. Johnson missed 38 days with left Achilles tendinitis and had appeared only as a pinch hitter since coming off the disabled list on Sept. 10.
Dan Uggla struck out looking with runners on first and third to end the second inning. Uggla also took called third strikes from Lee in the fifth and eighth innings, giving the slumping second baseman a franchise-record 170 strikeouts, breaking his own mark. He had 168 strikeouts in 523 at-bats in 2012. The fourth-inning strikeout came in his 445th at-bat.
Uggla, Justin Upton (158) and B.J. Upton (151) rank third through fifth in the National League in strikeouts.
NOTES: The game lasted 2 hours, 7 minutes. ... Lee set his career high with 16 strikeouts in a 5-0 loss to the Braves on May 6, 2011. ... Braves C Brian McCann, who left Thursday night's game against the Phillies with an adductor strain, was held out and is not expected to start in the final two regular season games. Still, manager Fredi Gonzalez said McCann is expected to be ready for the postseason. ... Gonzalez said he hopes RHP Jordan Walden (shoulder) can throw an inning this weekend. Walden has not pitched since allowing four hits and three runs in one inning against Washington on Sept. 17. ... Phillies manager Ryne Sandberg said RHP Ethan Martin "most likely" will start on Saturday against Braves LHP Mike Minor.