That stopped Souths' comeback in its tracks.A Jamie Lyon penalty goal soon after gave Manly an eight-point buffer they held for the rest of the contest.
The win was Manly's third in a row and keeps intact their September dreams.
They are four points behind eighth-placed Penrith but face Newcastle and Parramatta over the next fortnight.
Manly skipper Lyon could find himself in trouble with the NRL after he appeared to question the integrity of the match officials when he remarked to referee Henry Perenara after a series of penalties against Manly: "It seems like you are trying to get them back into the game."
Manly completely dominated the first half, as Souths struggled for momentum on the back of a series of handling errors, in particular by Joe Burgess.
Lyon crossed first for the visitors from a Daly Cherry-Evans pass in the just the fourth minute.
Lyon added a penalty goal minutes later before a Jorge Taufua try in the 24th minute gave Manly a 12-0 lead.
Trbojevic was the best player on the field in the first stanza and scored a deserved try five minutes from the break for Manly to lead 18-0 at halftime.
But Souths came surging back in the second half, with halfback Adam Reynolds leading the way.
The NSW playmaker scored himself in the 46th minute and then grubbered for Cody Walker's try five minutes later.Joe Burgess then had his try disallowed and that was Souths' night.
Souths coach Michael Maguire couldn't believe the no-try call against Burgess.
"They are defining moments in the game," he said.
"We made it hard for ourselves in the first half but we achieved what we wanted to in the second half, getting our completions up but those sorts of things in the game are defining moments.
"You say you thought it was a try and I did think the same."Manly coach Trent Barrett found it hard to keep a straight face when he said he thought it wasn't a try.
"The last month we have been terrific and tonight was an extremely important two points for us," he said.
"It was an extremely important game for them in terms of keeping their season alive.
"We still have some work to do, we can't be looking at the table."Our first half tonight was really good. The second half was a scrappy affair but we defended our tryline well."
Souths centre Bryson Goodwin injured the arm he broke earlier this year.
Manly winger Matt Wright suffered a second half ankle injury.
- AAP