Manly held an emergency meeting on Monday night with the players in question. The club will now face the Roosters without them.
Coach Des Hasler had told his players he would support their decision to stand down from Thursday's game over the pride jersey, the SMH reported.
Manly will become the first club in rugby league history to wear a jersey celebrating inclusivity, with rainbow colours replacing the traditional white piping.
The Sea Eagles' major sponsor is gambling company Pointsbet, while their home stadium, 4 Pines Park, is named after an alcoholic brewing company.
Sea Eagles great Ian Roberts, the first rugby league player to come out as openly gay, was left heartbroken by the player revolt.
"I try to see it from all perspectives but this breaks my heart," Roberts said to The Daily Telegraph.
"It's sad and uncomfortable. As an older gay man, this isn't unfamiliar. I did wonder whether there would be any religious pushback. That's why I think the NRL have never had a Pride round.
"I can promise you every young kid on the northern beaches who is dealing with their sexuality would have heard about this."
Social media also erupted over the players' decision.
Wide World of Sports' Matt Bungard wrote: "I don't want to hear one single thing about 'respecting other people's opinions' or using religion as a crutch to hide behind while being homophobic. No issues playing at a stadium covered in alcohol and gambling sponsors, which is also a sin. What a joke."
Spalk Talk's Tom Read wrote: "As a manly fan, I'd be more than ok for those players to not play in this game, or ever again for the club."
Townsville Bulletin editor Chris McMahon wrote: "I don't care if it derails Manly's season, but if these flogs pull out of this game because of an inclusive jersey, they should be stood down for the season without pay. As a massive @SeaEagles supporter this is enough for me to almost pack it in."
