While Daly Cherry-Evans firmed in his chances to overcome a back spasm on Thursday, Trbojevic spent about 45 minutes completing running drills.
Medical staff then made the call to rest Trbojevic from Sunday's match, with the club expecting him to face Parramatta in round four.
Scans had cleared Trbojevic of a fourth tear in his left hamstring, after he left the field early in Friday's loss to the Warriors.
But with the 28-year-old having also had three injuries in his right hamstring, Manly have decided to leave him on ice.
Lehi Hopoate is expected to play fullback in Trbojevic's absence, while Clayton Faulalo or Tommy Talau will likely play wing.
"We can trust Lehi to do just as good," prop Taniela Paseka said.
"If we know he's not playing we can prepare for that. (Lehi) is such a great fill-in and a good fullback too."
Manly's call came as players lauded Cherry-Evans' durability, with the veteran half increasingly likely to face Canberra.
Six days after struggling to move in the Sea Eagles' loss to the Warriors, Cherry-Evans trained freely with teammates on Thursday at Brookvale.
After a calf cork changed his running style, the Manly captain looked every bit his 36 years of age as he fell to the ground twice and struggled off the field.
But any thought of long-term concerns have been quickly put to bed, with Cherry-Evans taking part in contact on Thursday while also kicking and moving freely.
"He's probably the most professional athlete or person I know," Paseka said.
"He's just a battler. He never wants to let the team down. I could see early in the performance against the Warriors, it was bothering him.
"He could have gone off earlier, but he knew that if he went off it would have been a very tough game for us.
"It just shows how tough he is upstairs and what this club means to him and this team means to him. He's just a tough bastard."
The only player in the NRL born in the 1980s, Cherry-Evans' only injury lay-off in the past nine years was an ankle issue that ruled him out for a month in early 2019.
Beyond the fitness of their two most important players, Manly's other big issue remains consistency.
Their win over North Queensland was hailed by Cooper Cronk as the best opening-round performance he had seen, before they were shocked by the Warriors.
That has typified Manly's recent seasons after they beat each of last year's top-three teams on the ladder, but lost to all of the bottom three.
"We're still trying to figure out (the issue)," Paseka said.
"This is my seventh or eighth year here and you think you know (what causes it).
"And then when it comes, it's just so hard to figure it out. I think we're getting closer.
"When you have a good game you've got to remember to not ride the highs too high and stay neutral. Maybe that's what we did."
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