The former national captain stands down as Wales revamp their back-row following the disappointing 18-18 draw against Italy last weekend.
Alix Popham comes in at number eight with skipper Michael Owen moving across to the blindside flank.
Behind the scrum Michael Phillips makes his first Six Nations start in place of injured scrum-half Dwayne Peel. And on the right wing Dafydd Jones is drafted in to replace Scarlets team-mate Mark Jones, who has been ruled out following a minor knee operation.
On the replacements bench, Dafydd Jones covers the back row with Bath's Andy Williams deputising at scrum-half.
Although 84-cap Charvis goes out of the 22, Johnson believes it does not necessarily signal the end of the 33-year-old's international career.
Johnson, who still has to make a decision on his future as Wales coach, revealed: "Colin's been a true professional about it.
"He has been a true professional in the time I have dealt with him, but he just looks a player that is tired.
"He has played a lot of rugby this year the best part of 20 games already missing just one game for Newcastle in the Guinness Premiership and featuring for us at international level throughout the campaign so far this autumn.
"We are resting him, but he will remain part of the squad and we want him around to help lift the players. I think it's fair that he has a break because I don't want to throw the boy out there again. At the moment he is tired.
"I don't see it as the end for him. With his age there is always going to be a question mark, but he has to be handled well when you consider the workload of a modern international."
Johnson defended his decision to keep Gavin Henson on the replacements bench, saying the Ospreys star has had too little rugby since coming back from suspension.
"If Gavin Henson was your son would you throw him in against France in front of everyone at the Millennium Stadium? What's the kid going to gain by that? The reality is it's not going to happen on my shift. It's not fair on the kid and therefore it is not fair on the team."
France coach Bernard Laporte has warned his players to beware of a Wales backlash in Cardiff.
Les Bleus can all but guarantee their third Six Nations title in five years with a victory. But Laporte reckons this weekend's contest could be the toughest so far for his team.
"If we want to win the Six Nations, we have to put in just as big an effort as we have done so far. It will be a difficult game because Wales have not had a great tournament and they would like to finish well at home. We have to be at 100% if we want to win."
Laporte has made just one change to the side that crushed England 31-6 in Paris last Sunday, Bourgoin's Julien Bonnaire promoted from the bench into the back row in place of veteran Olivier Magne.
Magne takes his place among the replacements while Bonnaire will team up with Thomas Lievremont and Yannick Nyanga at the base of the scrum.
Scotland coach Frank Hadden has made three changes to his line-up as his team sign off from this season's RBS 6 Nations Championship against Italy in Rome.
Chris Cusiter and Gordon Ross have both been drafted in for their first Six Nations starts of the season while hooker Scott Lawson is back in the team at hooker after featuring in the game against Wales.
They replace Mike Blair, Dan Parks and Dougie Hall respectively, who have dropped down to the replacements' bench following the 15-9 defeat to Ireland at Lansdowne Road last weekend, while Scott Murray will win a record-equalling 75th cap against the Italians, drawing level with Gordon Bulloch.
FRANCE (v Wales): T Castaignede (Saracens), A Rougerie (Clermont Auvergne), F Fritz (Toulouse), D Traille (Biarritz), C Dominici (Stade Francais); F Michalak (Toulouse), D Yachvili (Biarritz); S Marconnet (Stade Francais), R Ibanez (London Wasps), P De Villiers (Stade Francais), F Pelous (Toulouse), J Thion (Biarritz), Y Nyanga (Toulouse), T Lievremont (Biarritz), J Bonnaire (Bourgoin)
Replacements: D Szarzewski (Stade Francais), O Milloud (Bourgoin), L Nallet (Castres), O Magne (London Irish), J-B Ellisalde (Toulouse), L Valbon (Brive), C Heymans (Toulouse).
WALES (v France): L Byrne (Llanelli Scarlets); D James (Llanelli Scarlets), H Luscombe (Newport Gwent Dragons), M Watkins (Llanelli Scarlets), S Williams (Ospreys); S Jones (Clermont Auvergne), M Phillips (Cardiff Blues); Duncan Jones (Ospreys), R Thomas (Cardiff Blues), A Jones (Ospreys), I Gough (Newport Gwent Dragons), R Sidoli (Cardiff Blues), M Owen (capt, Newport Gwent Dragons), M Williams (Cardiff Blues), A Popham (Llanelli Scarlets).
Replacements: M Davies (Gloucester), G Jenkins (Cardiff Blues), J Thomas (Ospreys), Dafydd Jones (Llanelli Scarlets), A Williams (Bath), N Robinson (Cardiff Blues), G Henson (Ospreys).
SCOTLAND (v Italy): H Southwell (Edinburgh Gunners); C Paterson (Edinburgh Gunners), M di Rollo (Edinburgh Gunners), A Henderson (Glasgow Warriors), S Lamont (Northampton); G Ross (Leeds), C Cusiter (Border Reivers); G Kerr (Leeds), S Lawson (Glasgow Warriors), B Douglas (Border Reivers), N Hines (Perpignan), S Murray (Edinburgh Gunners), J White (Sale Sharks, capt), A Hogg (Edinburgh Gunners), S Taylor (Edinburgh Gunners).
Replacements: D Hall (Edinburgh Gunners), C Smith (Edinburgh Gunners), A Kellock (Edinburgh Gunners), J Petrie (Glasgow Warriors), M Blair (Edinburgh Gunners), D Parks (Glasgow Warriors), S Webster (Edinburgh Gunners).