South Sydney Rabbitohs were left fuming over a controversial bunker decision to deny them a late equalising try they believe cost them the game and potentially ended their poor season.

The Rabbitohs were on the cusp of sealing an unlikely comeback against Manly Sea Eagles when they appeared to have drawn level through Joe Burgess before eventually losing 20-12.

The video referees overturned the on-field decision to award Burgess a late try that could have made it 18-all after judging the winger to have knocked-on while grounding, despite replays appearing inconclusive.

While a loose carry, Burgess appeared to still have contact with the ball while grounding for a try that Souths' coach Michael Maguire says lost his club momentum and a chance to seal a comeback.

"They're defining moments in the game," Maguire said. " Obviously I need to have a chat with the refs about what they saw in that."

It summed up a disappointing night for South Sydney who suffered their eighth consecutive defeat in front of a meagre attendance that led to a rare sight at Allianz Stadium. For perhaps the first time at a non-finals NRL match, Manly Sea Eagles had more fans than an opposition at the football stadium.

That it happened just three kilometres from the spiritual home of one of the game's most historic clubs was even more telling of the Rabbitohs plight and the defeat vindicated the protest made in absentia by their members.

Manly captain Jamie Lyon opened the scoring for the Sea Eagles after finishing a set move than required a brave call from the bunker to approve. Forward Jake Trbojevic stopped running as the decoy, opening up a case for South Sydney Rabbitohs to claim for an obstruction, but not sufficient to overrule the original decision.

A penalty midway through the first half extended the Sea Eagles lead to eight before some Jorge Taufua brilliance put Souths in danger of extending their losing streak to eight games. The Manly winger cleverly beat three opponents, dancing on his way to the try-line.

It wasn't even half-time when those few Rabbitohs' fans were bracing themselves for their club's worst run of results in eight years. Slack marking allowed Jamie Buhrer to burst through the line before finding Tom Trbojevic in support who scored their third try, making it 18-0 by the first break.

The Rabbitohs found an unlikely way back into the match when Adam Reynolds slipped through a weak tackle by two forwards 20 metres out from the line, allowing the Origin half to dart his way for a try and cut the deficit to 12.

Reynolds turned provider to give Souths more than a glimmer of hope of clinching an unlikely fightback when he set-up Cody Walker to suddenly make it a six-point game. A cheeky grubber deceived Manly's backline, allowing the Rabbitohs fullback to race through and score beneath the crossbar.

Entertainment born from horrendous defending gave those few fans that did attend something to admire but the Rabbitohs were seething to have been denied a third try after Joe Burgess was cruelly ruled to have knocked-on while grounding a try. It appeared to be a certain four-pointer for the English winger only for the bunker over-ruled the on-field decision, judging Burgess lost control.

The home fans went from being irate to deflated within a matter of minutes when Luke Keary killed Souths' momentum with a careless foul off the ball. It gave Lyon a chance to extend Manly's lead to eight points with a penalty goal.

With that came the end of any sense of composed football. Wayward passes, knock-ons and senseless penalties became the norm as two teams not accustomed to winning seemingly showed their poor sense of finishing. However, it was South's inability to control the football in the final minutes that prevented them from clinching a comeback, consigning the club to their 13th defeat of the season.