The decision to send Manly star Jake Trbojevic to the bin with 13 minutes to play was one of the biggest calls made by a referee all season, but the NRL believes it was the right one.
Trbojevic was binned for a professional foul on Dane Gagai, as Souths were on the break and looking for a way back into the match.
Manly led 26-20 when Trbojevic was given his marching orders, although the Bunnies scored twice while he was on the sidelines, storming home to a 34-26 win.
Despite Des Hasler blowing up at the decision, NRL head of football Graham Annesley backed in the decision, saying Trbojevic left the referees with no choice.
"It was a professional foul in a try-scoring situation," Annesley said post-game.
"Last week I publicly criticised a referee for not using the sin bin in similar circumstances.
"If Jake doesn't grab the support player, the consequences don't occur."
Hasler said his side were "dudded", suggesting the penalty was fair, but the sin-binning was too much.
"Do I think we were dudded? Yep, I think we were dudded," Hasler said.
"The call on Jake in the second half was a bit tough.
"Was it a penalty? I don't mind a penalty. I can handle a penalty. Did he deserve to get sent off? No, I didn't think he deserved to get sent off.
"You don't want to see the game coming down to crucial calls like that."
The Rabbitohs will now face Canberra next weekend for a spot in the grand final.