Medlen (6-1) extended his scoreless streak to 28 1/3 innings and nailed down the Braves' third win in their last four games.
Chris Kimbreal closed out the game for his 32nd save.
Andrew Werner (1-1) took the loss despite a solid six-inning start. Werner was charged with two runs on four hits and fanned seven as the Padres' eight-game winning streak came to an end.
Everth Cabrera had two of San Diego's six hits.