Perdomo, 24, allowed nine runs (seven earned) in three innings in a 13-4 loss to the Los Angeles Dodgers on Wednesday. His ERA jumped to 8.36 in the process, and he has surrendered 26 hits, nine walks and 13 earned runs in 14 innings.
His place on the roster was taken by right-handed reliever Kirby Yates, who came off the 10-day disabled list.
Perdomo was 8-11 with a 4.67 ERA a year ago in his second season in the majors. He went 9-10 with a 5.71 ERA the previous season as a Rule 5 selection plucked off the Class A roster of the St. Louis Cardinals' farm system.
Perdomo, 24, was involved in last week's brawl with the Colorado Rockies, resulting in a five-game suspension that he served.
Yates, 31, pitched 3 2/3 scoreless innings over five appearances for the Padres in the season's first 10 days before sustaining an ankle injury.
--Field Level Media