Peralta (5-8) won for the second time in his past eight starts, giving up two singles to go with four strikeouts and four walks.
Francisco Rodriguez pitched the eighth and Jim Henderson the ninth for his 10th save. Rodriguez picked up the previous five saves for Milwaukee to reach No. 299 in his career while Henderson was on the disabled list.
Segura finished with three hits, including his 11th homer of the season, and Norichika Aoki added three singles after the birth of his son Thursday.
Atlanta was shut out for the 10th time and lost for the fourth time in five games.
Julio Teheran (5-4) gave up two earned runs on eight hits in 6⅓ innings. He struck out five and did not allow a walk.
Segura’s solo homer to lead off the fifth gave Milwaukee a 2-0 lead.
In the first, Aoki and Segura singled before Carlos Gomez was hit by a pitch to load the bases. Aramis Ramirez gave Milwaukee a 1-0 lead on a sacrifice fly. Gomez was picked off first and Juan Francisco popped out to end the rally.
Atlanta struggled to score for the second night in a row.
After stranding 11 runners in a 4-3 loss at the New York Mets on Thursday, Atlanta was at it again.
After the first two batters in the third – Dan Uggla and Chris Johnson – were walked, Teheran tried a sacrifice bunt that turned into a force out at third. Andrelton Simmons flew out and Jason Heyward grounded out to end the inning.
In the fifth, Atlanta picked up its first hit of the game when B.J. Upton led off with a single.
He took second when Uggla flew out to deep center field and advanced to third on an infield single by Johnson.
This time, Teheran attempted a safety squeeze and bunted the ball to the right side of the plate. Peralta was able to field the ball in his glove and quickly tossed it to catcher Martin Maldonado, who tagged out the sliding Upton. Simmons followed with a fly ball to the right-center field gap that was caught by a diving Aoki.
Atlanta also had runners at first and second with two outs after Henderson walked Justin Upton and B.J. Upton in the ninth, but Uggla flew out to center to end the game.