Kenny Bromwich, who was slated to be 18th man, has also pulled out of Friday night's clash in Sydney.
Sean O'Sullivan comes into the side to replace Nikorima while prop Josh Kerr is on the bench in place of Nicholls.
Concern for family members being left behind, and the fact their homes are in the firing line of the cyclone, were behind the players' decisions to stay at home and not leave with the team on their flight to Sydney on Wednesday evening.
Their decision has the blessing of the club.
Nicholls was seen sandbagging his home on Wednesday. He has a young family and lives in the Redcliffe suburb of Newport, which is expected to feel the brunt of Cyclone Alfred when it hits land between Brisbane and the Sunshine Coast on Friday morning.
The Dolphins and Rabbitohs showdown, originally slated for Suncorp Stadium, was shifted out of Brisbane to Sydney's CommBank Stadium.
Bree Nikorima, the partner of Dolphins playmaker Kodi Nikorima, is six months pregnant and has two young children.
She took to social media to lash the NRL for families being left behind during a cyclone to play a game of football, labelling the move "disgusting" in a now-deleted story on Instagram.
She also made the point her home is prone to flooding.
Brisbane and Dolphins club bosses have made moves to ensure the safety of staff and players' families left behind.
The Broncos flew to Sydney on Tuesday to prepare for Thursday night's NRL clash with Sydney Roosters at Allianz Stadium and are scheduled to return on Friday.
Loved ones of players and staff from both clubs face nervous days.
Brisbane CEO Dave Donaghy has flown back to the Queensland capital from Sydney to oversee support.
Donaghy's Dolphins counterpart Terry Reader said the NRL had helped the club with their contingencies.
"Any of our players and travelling staff's partners that are worried about not having their partners around, we are going to put them up in a hotel in the city so they have more security around being with each other," Reader said.
The Bureau of Meteorology's technical bulletin has warned there is a possibility, although low, of the Category 2 cyclone becoming a low-grade Category 3 as it gathers momentum.
With 26,000 homes in danger of flooding, the Broncos will ensure those left behind have the support needed to prepare for what may unfold.
Broncos coach Michael Maguire addressed the situation on Wednesday morning in Sydney when he fronted reporters.
"The club has been really proactive," Maguire said.
"Our chief executive (Donaghy) flew down (to Sydney) last night and turned around and went straight back to town to make sure everyone is safe while the team is down here.
"They are talking to and getting out to the partners and the wives to make sure they are safe through this situation."
Reader said he "absolutely" understood the sentiments of Bree Nikorima.
"Everyone is apprehensive about what is happening and we are making sure we do everything we can to make everyone more comfortable and put our players' and partners' minds at ease," he said.
Dolphins players had the day off on Wednesday to make sure their families are well prepared, while the club's welfare team will oversee the situation until the team returns.
The AFL postponed its two opening-round fixtures in Brisbane and the Gold Coast, initially scheduled for Thursday and Saturday night.
Brisbane Roar's A-League Women clash with Melbourne City, scheduled for Sunday at Brisbane's Perry Park, has also been postponed.
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