Bochy was to sit out Wednesday's game against the Pittsburgh Pirates in the wake of an incident in Tuesday's contest when Kontos was determined to have intentionally thrown at pitch at Pittsburgh's Andrew McCutchen.
Kontos, send down to Class AAA Fresno Wednesday, will serve a three-game suspension upon his return to the major leagues, MLB officials announced.
He was also fined an undisclosed amount.
Umpires had warned both teams before McCutchen was hit with the pitch.
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