La Rochelle - France's minor premiers last season - celebrated a 16-9 home win over Racing 92 in a seventh round match on Sunday.
Carter has not played for three weeks and his absence prompted L'Equipe newspaper rugby writer Richard Escot to speculate that Racing were "undoubtedly preserving" Carter and former Springbok Patrick Lambie for upcoming European Cup matches against the Leicester Tigers and Irish province Munster.
Maxime Machenaud, who replaced Carter at first five-eighths, scored all Racing's points with three penalties to ensure a defensive bonus point.
La Rochelle claimed the game's only try - to substitute Vincent Rattez.
Rattez replaced veteran Australian first five-eighth Brock James, who left the field with an injury, leaving him in doubt for La Rochelle's Champions Cup games.
The defeat to La Rochelle left Racing 92 in eighth place on 16 points - 11 points behind leaders Lyon.
Toulouse moved up to third place after a 28-18 win over champions Clermont Auvergne, who fielded former Counties and Chiefs Backrower Fritz Lee at No 8.
Stade Toulouse rested former All Blacks prop Charlie Faumuina but were still too strong for Clermont, scoring three tries to two with 20-year-old French test halfback Antoine Dupont claiming a first half brace.
Australian first five-eighth Zack Holmes got Toulouse's third try early in the second half.
Lyon lead the Top 14 standings after seven rounds with 27 points, followed by Montpellier (24), Toulouse (24), La Rochelle (22) and Bordeaux-Begles (22).
Photo by: GETTY IMAGES (Caption: Dan Carter missed his third consecutive game as French Club Racing 92 lost at La Rochelle