The referee had missed the incident which came after Muscat elbowed O'Donovan. Both players were booked by the official with Muscat suspended for two games on Tuesday for his role in the altercation.
Mariners chief executive Shaun Mielekamp said the club would appeal the decision.
"We are extremely disappointed at the decision," he said.
"The disparity in sanctions issued for this match highlights the flaws in the system.
"The media circus around the incident has had a high impact on the result and we will look at our various avenues for appeal."
(Writing by Patrick Johnston in Singapore; editing by Amlan Chakraborty)
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