Ntamack, 24, will miss this year's World Cup after rupturing cruciate ligaments in his left knee in last weekend's win over Scotland.
La Rochelle's Antoine Hastoy was given the chance to start at fly-half with Bordeaux-Begles' Matthieu Jalibert on the bench.
The pair are fighting to start the World Cup's opening game with New Zealand on September 8 in Paris instead of Ntamack.
Fiji winger Josua Tuisova, who has played his club rugby in France since 2013, withdrew from the game in Nantes earlier in the day with Toulon's Jiuta Wainiqolo taking his place.
The hosts led 9-3 after 20 minutes as full-back Melvyn Jaminet, putting his hand up to be named on Monday in Fabien Galthie's World Cup squad, kicked three penalties before Caleb Muntz responded for the visitors.
Galthie's side took hold of a loose affair by the break as hooker Peato Mauvaka and prop Uini Atonio crashed over either side of Tevita Ikanivere's try for Fiji and Les Bleus had a 21-10 advantage.
Toulouse's Jaminet, battling with Brice Dulin for a place in Galthie's squad, made it 24-10 with a 42nd-minute penalty before Fiji captain Semi Radradra cut the deficit with a trademark bulldozing effort.
Muntz converted to make it 24-17 with half an hour to play in humid conditions at Stade de la Beaujoire.
With a quarter of the game remaining, France ended Fiji's hopes of a second straight win in the fixture as flanker Sekou Macalou intercepted Frank Lomani's pass to run in from almost 50 metres.
Jaminet took his tally for the game to 16 points with a conversion before Hastoy was replaced after a quiet performance for Jalibert, the favourite to stand in for Ntamack, with the score at 31-17.
The full-back kicked another penalty with 10 minutes to play as Mauvaka moved to No. 8 and took over as captain with Gregory Alldritt off.
Fiji then failed to claim a late consolation try as they lost possession at a lineout near the France line less than three weeks from the start of the World Cup.
They finish their preparation for the tournament at England next weekend before starting their World Cup campaign against Wales on September 10.
Hosts France have just one game before facing the All Blacks, with next Sunday's game with Australia in Paris.
