Wilkinson has been axed for only the third time in his 12-year international career after Johnson decided to revamp his back division for Saturday’s clash with Grand Slam-chasing France.
The heavy blow to the head Wilkinson suffered in last weekend’s 15-15 draw with Scotland has limited his preparation time but the 30-year-old has been struggling for form all tournament.
Toby Flood will start at fly-half in Paris in one of four changes to England’s line-up behind the scrum.
Full-back Ben Foden, debutant winger Chris Ashton and veteran centre Mike Tindall all come in at the expense of Delon Armitage, the injured Ugo Monye and Mathew Tait.
Wilkinson had only been chopped from the England team on two previous occasions – for Paul Grayson at the 1999 World Cup and for Danny Cipriani in the 2008 Six Nations.
England boss Johnson insisted Wilkinson remains central to England’s 2011 World Cup plans.
“Jonny is still a world-class player. If I thought Jonny was on the decline, I wouldn’t have picked him for our last seven internationals,” said Johnson.
“There’s not many players in world rugby who could have dropped that goal against Ireland in the last 10 minutes.
“I’m sure Jonny will be disappointed he’s not starting but he’s a team player. The guys on the bench will be playing in the last quarter and that’s the most important quarter of the game.
“We need at least two players in every position and we would have been happy to pick Toby in every game so far.
“Toby has been an on-field general for us in the past two years. He is graduating into the leadership camp for us as he gets more experience.
“Ahead of a World Cup, he needs to play in that position over the next 18 months as well as Jonny.”
Flood, who was Wilkinson’s understudy at Newcastle, played fly-half against France at Twickenham last year when England scored five tries in 42 minutes and routed Les Bleus 34-10.
But on that occasion Wilkinson was not fit.
“It’s a big honour for me to go out there and play (number) 10 for England,” said Flood.
“Getting picked ahead of a guy who is ultimately world class and has been the leader of the team in that position for a long, long time is great.
“By no means does that mean he is finished though because we all know how hard he bites when he gets batted down. We’ve all been dropped, obviously he’s been dropped less than others, but it’s about how you act in the dark times that makes you the person you are.
“He came up and said, ‘If there’s anything you need, let me know’. He’s shown a huge amount of character.”
Foden gets a long-awaited chance to make his first Test start after England finally bit the bullet and dropped the out-of-sorts Delon Armitage, who failed to make the final 22.
Ashton will make his Test debut in place of Monye, who damaged his neck at Murrayfield, and he comes into the team after an electric run of 19 tries in 25 games for Northampton this season.
Tindall, who only recently returned from four months out with a hamstring injury, has been recalled to combat the destructive French centre Mathieu Bastareaud.
“Mike coming into the centre is a tough call on Taity, who hasn’t done much wrong but Mike brings a physical edge,” said Johnson.
“And Ben’s form has been so good we have included him at full-back. Delon has not been playing as well as he can. That was a good call for Ben, who is playing very well. Chris Ashton’s form has been very good.”
Up front, Lewis Moody has returned at openside flanker with Joe Worsley switching to blindside and James Haskell moving to the bench.
Simon Shaw has recovered from a shoulder injury which kept him out of the Scotland game and starts in the second row, but there remain doubts over the fitness of captain Steve Borthwick who missed training yesterday with a knee injury.
England have beaten France in each of their last three meetings, including two games in Paris – the 2007 World Cup semi-final and the 2008 Six Nations.