Santana (10-6) gave up only five hits -- all singles -- and matched a career high with 11 strikeouts over eight innings. Craig Kimbrel struck out the side in the ninth to earn his 32nd save of the season.
Evan Gattis had three hits and knocked in both Atlanta runs.
The Braves took three of four from San Diego to finish their longest homestand of the year at 6-5.
Recalled from Triple-A El Paso to make a spot start for the injured Ian Kennedy, Jason Lane (0-1) tossed six scoreless frames before Gattis homered to lead off the seventh. The lefty allowed six hits overall, struck out two and issued no walks in six-plus innings.
Lane, the oldest pitcher to make his first MLB start in Padres history at 37 years and 219 days old, played as an outfielder for Houston and San Diego from 2002-07.