A shattered Trbojevic was escorted by three Sea Eagles medical staff up the CommBank Stadium tunnel, after falling awkwardly on his left arm and immediately wincing in pain.
Manly will wait on scans before making a full prognosis, but there are already fear's the game's most electric player will battle to run out again this season after copping the blow.
It came on a brutal night for the Sea Eagles, with coach Des Hasler fuming over a late high-tackle call that put the Eels on the attack for a late match-winning try.
But the bigger pain for Manly, NSW and the NRL as a whole will still be Trbojevic.
The Blues are already without Latrell Mitchell, Ryan Papenhuyzen, Cameron Murray, Dale Finucane and Victor Radley, but Trbojevic's injury is the most crucial of the lot.
The fullback had been the Sea Eagles' best before he went down in the 64th minute, having a hand in two tries and looking back like his old self.
But he came undone when he chased back on a grubberkick and jostled with Marata Niukore, before going to ground.
Trbojevic and brother Jake cut a dejected figure in Manly's sheds after the match, going as far as to apologise to teammates after the loss.
"He takes it very hard," Hasler said.
"He blames himself a lot. But he is just having one of those runs at the moment. He'll bounce back."
Trbojevic had earlier been Manly's best, shrugging off concerns over his knee and a corked thigh to inject himself into the match.
His quick hands helped Reuben Garrick over for Manly's first, while he split the line open to put Manly clear in the second half by putting Morgan Harper over with Mitch Moses in the sin-bin.
The Sea Eagles were out to a 20-10 lead when Reuben Garrick chased down a Kieran Foran kick, and looked set for a crucial win.
But it was then Parramatta responded.
Expansive football put Tom Opacic over with 20 to play, and when Trbojevic exited it always looked like a mission impossible for the Sea Eagles.
They were down to 12 men when Sean Keppie was sin-binned for a dangerous throw, and Manly then fumed when Christian Tuipulotu was penalised for a high shot on Hayze Perham.
Perham had slipped as neared the sideline, and Tuipulotu sent him over it with force before the bunker intervened.
From the next attacking raid the Eels went left, Isaiah Papali'i put Will Penisini over and Moses nailed a sideline conversion in the penultimate minute to win it.
"It wasn't high. It was a good tackle. It was a brave tackle. They're called a try save," Hasler said.
"The idea of the game is defence and the idea of a try save is to come up with big plays.
"It was a great play. It just adds to the disappointment on the result. On the back of a 9-2 penalty count. They got legged back into the game."
Eels coach Brad Arthur however was insistent the right call had been made.
"Hayze might have slipped, but at the end of the day if you make contact with someone in the head, you get penalised," Arthur said.
"We have, all year.
"We played the long game really well tonight. We were patient and calm ... It was true character we showed."
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