SAN DIEGO -- Pirates pitcher Angel Perdomo was suspended three games by Major League Baseball on Wednesday, one day after he hit Padres third baseman Manny Machado in the back with a 98 mph fastball. Perdomo's suspension was shortened to two days on Friday. He will rejoin the team on Saturday. Pirates manager Derek Shelton drew a one-game suspension and an undisclosed fine.

Shelton served his suspension Wednesday as the Pirates concluded a three-game series in San Diego, and Perdomo began his. Bench coach Don Kelly served as Pittsburgh’s acting manager on Wednesday.

Perdomo, who also was fined, was suspended for “intentionally throwing” at Machado, according to the announcement from Michael Hill, MLB’s senior vice president for on-field operations.

The left-handed reliever hit Machado with his first pitch following Juan Soto’s 418-foot home run in the seventh inning Tuesday night at Petco Park. The umpiring crew conferred and then ejected Perdomo and Shelton, who came out of the dugout to argue the pitcher’s ejection.

“I gave all my best to Soto, all my pitches,” Perdomo said after the game Tuesday. “He got the home run against me. And then against Machado, I just tried to come in and went too far in and hit him by mistake.”

Shelton on Tuesday also said the HBP was unintentional.

“Ball just got away from him; it hit him,” the manager said. “The umpires got together, which they’re supposed to do. After they got together, they decided on an ejection.”

Perdomo, 29, has a 3.92 ERA in 21 relief appearances this season. His absence leaves Jose Hernandez and Ryan Borucki as the Pirates’ lefties in the bullpen.