Furious Wellington coach Ernie Merrick has described O'Donovan's headbutt as "going back to the dark ages", saying he's never seen anything so blatant on a football field.
The Central Coast striker's nasty act took place during the second half of the Mariners' 3-1 mauling of the Phoenix.
Referee Kris Griffiths-Jones seemingly missed the headbutt that sparked a brief all-in melee and came moments after Muscat had raised his elbow to O'Donovan's head.
But instead of sending O'Donovan off, Griffiths-Jones stunningly showed the Irishman a yellow card - one of nine in the feisty affair.
It soured an otherwise absorbing show, enjoyed by a crowd of 10,073.
"I don't understand how someone can get away with that," an irate Merrick said.
"That's going back to the dark ages. I've never seen that so blatantly happen.
"I'll bet there's some rule somewhere that says because a player got a yellow card for that they got off for it.
"That was the most disgusting thing I've seen in a while."
Merrick also lamented the way Wellington lost the match.
While he admitted his side lacked impetus up front during the first half, he thought some decisions against them were unfair and said a questionable first-half penalty against Muscat killed their chances.
Muscat was judged by Griffiths-Jones to have brought down Josh Rose in the box in the 27th minute, resulting in the Mariners' first goal.
Replays showed him appearing to successfully win the ball, but the decision had been made and Fabio Ferreira duly converted from the spot.
"It was a clean tackle," Merrick said.
"Manny Muscat's got a reputation, but not since I've been at the club - he's changed completely."
Depending on other results, injury-ravaged Wellington could well slip out of the top six before this round is through.
RadioSport: Ernie Merrick on the O'Donovan headbutt
They will also be without key players Roly Bonevacia and Alex Rodriguez - both suspended after receiving their fifth yellow cards - and Roy Krishna, who injured his ankle.
For all the controversy and niggle, New Year's Eve was a night to celebrate for the last-placed Mariners, who finally notched their second win of the season and first in 11 matches and nearly three months.
Coach Tony Walmsley's prayers that the skilful Ferreira and pacy Mitch Austin would inject needed flair on their starting returns were answered.
The wingers combined well, and Austin scored the Mariners' second goal three minutes after Ferreira's first when O'Donovan ran unmarked down the right and crossed for the 24-year-old to open fire on Phoenix goalkeeper Glen Moss.
Wellington came to the party during the second half, forcing Mariners back-up keeper Tom Heward-Belle into numerous saves.
The 18-year-old did well but could not keep Blake Powell from making good on fellow substitute Matthew Ridenton's cross in the 67th minute to bring the score to 2-1.
But three minutes later Central Coast struck again, when Michael Neill pickpocketed the heavily marked Vince Lia in the danger zone and slotted into the bottom corner.
A content Walmsley said he hadn't seen O'Donovan's headbutt, but would look at it and deal with it internally if need be.
He said he couldn't tell whether the penalty was legitimate, but was happy to take it.
"We'll take anything we can get at the moment," Walmsley said.
- AAP