Fainga'anuku replaces Jordie Barrett (ankle) in the midfield, while Josh Lord comes into the lock position, with regular skipper Scott Barrett (leg laceration) not available for Saturday's clash.
Quinn Tupaea moves from outside to inside centre to accommodate Fainga'anuku, who came off the bench to great effect in the 26-13 win over Ireland in Chicago last weekend.
The other change to the run-on side sees flanker Wallace Sititi start in the back row of the scrum in place of Simon Parker, who drops out of the match-day 23.
Sam Darry (lock), Du'Plessis Kirifi (loose-forward) and Billy Proctor (centre) are among the replacements added to the bench.
The other Barrett brother, Beauden, remains at fly-half, with livewire Cam Roigard at scrumhalf. Caleb Clarke and Leroy Carter are the two wings, and Will Jordan continues at fullback.
Hooker Codie Taylor will scrum down with props Ethan de Groot and Fletcher Newell either side of him, while Fabian Holland partners Lord in the second row, and Peter Lakai is at number eight.
New Zealand have never lost a Test against the Scots, winning 30 of the previous 32 played since 1905. The two draws came in 1964 (0-0) and 1983 (25-25).
"We have a proud history with Scotland, and recent games between us have been close," New Zealand coach Scott Robertson said. "We have named the best team to reflect the challenge we know Scotland will present."
Tests between the sides have been reasonably rare, with only five in the past 17 years. Scotland have not toured New Zealand since 2000.
The Scots are celebrating 100 years of playing at Murrayfield this week and New Zealand will have to counter the occasion as well as a tough home side.
NEW ZEALAND TEAM:
15-Will Jordan, 14-Leroy Carter, 13-Leicester Fainga'anuku, 12-Quinn Tupaea, 11-Caleb Clarke, 10-Beauden Barrett, 9-Cam Roigard, 8-Peter Lakai, 7-Ardie Savea (captain), 6-Wallace Sititi, 5-Fabian Holland, 4-Josh Lord, 3-Fletcher Newell, 2-Codie Taylor, 1-Ethan de Groot
Replacements: 16-Samisoni Taukei'aho, 17-Tamaiti Williams, 18-Pasilio Tosi, 19-Sam Darry, 20-Du'Plessis Kirifi, 21-Cortez Ratima, 22-Billy Proctor, 23-Damian McKenzie
