The 32-year-old powerhouse will miss Sunday's showdown at Suncorp Stadium after failing a fitness test on Saturday afternoon.
Taumalolo had a knee cleanout at the end of the 2025 NRL season with North Queensland.
He trained with the Tonga side during the week in Brisbane but coach Kristian Woolf has taken a cautious approach and decided not to risk him against Samoa.
Veteran Felise Kaufusi will now start at lock with Tonga set to name a replacement on the bench, most likely an hour before kickoff.
Tonga can still make the Pacific Cup final on November 9 in Sydney even if they lose to Samoa, so long as they defeat New Zealand next week at Eden Park by the required margin.
AAP has been told Taumalolo may be rested next week if Tonga beat Samoa, to give him extra time to recover fully for the final. If Tonga lose he is more likely to play the Kiwis.
Taumalolo's absence will not stop Tonga fielding a strong pack, with Melbourne front-rower Stefano Utoikamanu to play his first game for the side after previously representing Samoa.
Another highlight for Tonga will be the Test debut of centre Robert Toia who was Dally M rookie of the year after a stellar season with the Sydney Roosters.
Toia was also a weapon for Queensland in their 2-1 series win over NSW in his debut State of Origin campaign.
Tonga coach Kristian Woolf, also in charge of the Dolphins, was impressed with Toia's game for the Roosters against his side at Magic Round and knew he would be a huge asset for the national team.
"Robert has had an outstanding year," Woolf said.
"When (the Dolphins) played the Roosters in Magic Round the way he competed with Herbie Farnworth who is one of, if not the best centre in the competition and the world, I thought Rob was really hard to handle that night and did a great job defensively as well.
"I knew he was Tongan and that pricked my interest a little bit. Then I watched how he performed during Origin against Latrell Mitchell and did such a great job.
"To be part of a winning Origin series, I think he is ready for this arena. I can't wait to see what he brings."