Perdomo gave up a home run to the Padres' Juan Soto in the seventh inning of Tuesday's game at San Diego. One pitch later, Machado was hit in the back by a 98-mph fastball from Perdomo, who was ejected.
"You give up a bomb like that, I would be mad, too, I'm not gonna lie," Machado said after Tuesday's game, a 5-1 Padres victory. "... I guess people don't respect people anymore."
In addition to Perdomo's discipline, which included a fine of an undisclosed amount, Pirates manager Derek Shelton was suspended one game.
Shelton was set to serve his suspension during Wednesday's game against the Padres. Perdomo's suspension also was set to begin Wednesday, pending a decision to appeal.
Perdomo, 29, is 1-1 with a 3.92 ERA in 20 2/3 innings this season, while allowing three home runs. He is 2-1 in his career with a 6.02 ERA in 43 relief appearances over three seasons for the Milwaukee Brewers (2020-21) and Pirates.