In one of the worst defeats of their five-year run, the Panthers fell behind 28-0 at halftime on Thursday night at Accor Stadium before eventually being beaten 28-18.
The four-time defending premiers at one stage looked likely to pull off a comeback, but were controversially denied a crucial Moses Leota try with 18 minutes to play.
Leota appeared to charge across the line and slam the ball down, only for bunker official Chris Butler to rule he had dropped it and there was no downward pressure.
Cleary believed afterwards the bunker had erred, and in turn killed off any momentum Penrith had in the second half while 28-12 down.
But still there are bigger concerns for the Panthers, after losing three games straight for the first time since 2019 and holding a 1-3 record after four rounds.
The Rabbitohs were impressive in the first half, with their left edge firing and Keaon Koloamatangi scoring a double.
Alex Johnston bagged a try in his return from a ruptured Achilles tendon, but didn't return after halftime with a shoulder injury that Souths do not believe is serious.
But Penrith were their own worst enemies, making errors in the lead up to all five of the Rabbitohs' tries.
So bad did it get, Cleary labelled it "comical" at times as his side completed just six sets and lacked any rhythm.Â
The Panthers also desperately missed Nathan Cleary and Dylan Edwards, as their replacements Trent Toelau and Daine Laurie had difficult nights at half and fullback.
Cleary will return next week and Edwards could join him, but Brian To'o finished Thursday with a hamstring injury and Scott Sorensen suffered a concussion.
Regardless, coach Cleary rejected the suggestion the club's player drain was starting to show, with the Panthers' top team and junior talent raided by rivals in recent years.
"I get the narrative, I get where you're going with this. I'm sure no-one is crying for us," Cleary said.
"But you haven't seen the real us yet. Once we do, then you can start making judgements on stuff like that."
Penrith have now lost games to the Sydney Roosters, Melbourne and Souths to start the season, after beating Cronulla in Las Vegas.
But most concerning is their defence, having conceded 118 points across the first opening rounds and more than they did in their first 13 games of 2021 combined.
"We just haven't got any rhythm in the way we're playing," Cleary said.
"We're going to need to find it really soon. Once we get that, we will have a better idea of how we're going."
Bennett, meanwhile, is pulling off an early-season miracle on his return at Souths.
They are 3-1 without Latrell Mitchell and Cameron Murray, with the former set to return in next Friday's blockbuster against South Sydney.
His return may mean Jye Gray drops out of the team, despite again being superb at fullback.
Koloamatangi led the way on the Rabbitohs' left edge, while Davvy Moale and Junior Tatola were both powerful in the middle.
Suddenly, Bennett has made a South Sydney side that was expected to struggle this year into one that has the NRL standing up and taking notice.
"I think they always stand up and take notice about South Sydney," Bennett said.
"There are too many quality players there when they're all together there. It's a team you can't underestimate.
"These are hugely important wins. Penrith had some wonderful players missing but so did we."
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