Dupuy will come on to the bench with Morgan Parra claiming Yachvili's starting spot where he will combine with Montpellier fly-half François Trinh-Duc.
France boss Philippe Saint-André revealed that he had taken the decision early to allow Dupuy as much time as possible to get used to being in the squad having not featured for France since November 2009.
"Above all we thought about the player, and tried to manage him but the pain would not go away," said Saint-André.
"To avoid affecting the preparation of this important game, I preferred to take the decision 48 hours before the match to allow the replacement to work with us for the next two days.
"The choice of Julien Dupuy seemed obvious to us given his international experience and his start to the season with Stade Français."
Yachvili added: "I don't feel at 100 per cent of my capabilities and I think it's sensible to rest and to get better to be fit again as quickly as possible to prepare for the next challenges with my club and with France."