Major League Baseball banned Manuel on Saturday, and he was to sit out the afternoon game when the Mets host the Pittsburgh Pirates. The amount of the fine was not disclosed.
On Thursday, Manuel argued with first-base umpire Bill Welke three times during the Mets' 7-5 win over the Philadelphia Phillies. He was ejected by Welke in the eighth following an obstruction call on Jose Reyes that let Shane Victorino slip out of a rundown.
Welke said Manuel "brushed" his hat with the bill of his own cap as he screamed in the umpire's face.
Bench coach Sandy Alomar Sr. was to manage the Mets on Saturday.
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