Cotter, who was given man of the match honours, will be fined between 10-13% of his Origin match fee for a crusher tackle on Blues winger Josh Addo-Carr in the 53rd minute.
Flegler, who was sin-binned in 69th minute for his shot on Tom Trbojevic that left the Sea Eagles fullback concussed, has been hit with a Grade 2 Careless High Tackle charge and faces a fine of between 13-20% of his Origin match fee.
Both Cotter and Flegler will be available for their NRL sides in Round 14.
Rabbitohs fullback Latrell Mitchell faces up to four matches on the sideline, while Roosters winger Dom Young and Dolphins utility Kurt Donoghoe are looking at three match bans.
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