The 31-year-old's selection had been the chief talking point in the All Blacks team in the build-up to the seventh edition of the World Cup, with Hawke's Bay full-back Israel Dagg assuming the starting role.
Dagg had been tipped to replace Muliaina after a superb return to top class rugby against South Africa in Port Elizabeth last month following a serious quadricep injury.
Richard Kahui and Isaia Toeava have been named on the wings, while Ma'a Nonu shifts to centre to allow Sonny Bill Williams to play inside centre in a huge backline to combat the physical Tongans.
Captain Richie McCaw will earn his 99th Test cap.
Wellington loose forward Victor Vito will start at number eight for the injured Kieran Read, while Jerome Kaino returns to the starting line-up after he missed the final Tri-Nations match against Australia last month to return home to be with his pregnant partner.
Tony Woodcock was named to start at loosehead prop, despite aggravating an old hamstring injury at training this week and being a doubt as last as Tuesday when assistant coach Steve Hansen told reporters the prop was a concern.
NZ: 15-Israel Dagg, 14-Richard Kahui, 13-Ma'a Nonu, 12-Sonny Bill Williams, 11-Isaia Toeava, 10-Daniel Carter, 9-Jimmy Cowan, 8-Victor Vito, 7-Richie McCaw (captain), 6-Jerome Kaino, 5-Ali Williams, 4-Brad Thorn, 3-Owen Franks, 2-Andrew Hore, 1-Tony Woodcock.
Tonga: 15-Vungakoto Lilo, 14-Viliame Iongi, 13-Sukanaivalu Hufanga, 12-Andre Ma'ilei, 11-Siale Piutau, 10-Kurt Morath, 9-Taniela Moa, 8-Viliami Ma'afu, 7-Finau Maka (captain), 6-Sione Kalamafoni, 5-Joseph Tuineau, 4-Paino Hehea, 3-Taufa'ao Filise, 2- Aleki Lutui, 1-Soane Tonga'uiha.