Padres reliever Ron Marinaccio was given a three-game suspension for intentionally hitting Orioles shortstop Gunnar Henderson, and San Diego manager Craig Stammen was handed a one-game ban.
Marinaccio has chosen to appeal the suspension, so his discipline will be held in abeyance until the process is complete.
Stammen will serve his suspension as the Padres play the St. Louis Cardinals on Monday.
The Padres appeared to throw at Henderson in the seventh inning, but missed with multiple pitches. Marinaccio then hit the 24-year-old with a first-pitch fastball in the ninth.
Marinaccio was immediately ejected, and Stammen was eventually tossed after coming out to argue.
San Diego appeared to be retaliating to Baltimore starter Trey Gibson hitting Xander Bogaerts in the head in the fifth.