The Harlequins scrum-half was rated as a certainty to feature among Johnson's 30-man party that will head to New Zealand on August 29.
But 24-year-old Care will undergo surgery on Thursday to repair a damaged joint in his left big toe suffered during last Saturday's defeat against World Cup warm-up opponents Wales at the Millennium Stadium.
England's medical staff anticipate that Care, who has won 32 caps, will be sidelined for six weeks.
With Johnson confident that last season's Six Nations number nine Ben Youngs will be fit and available after having a knee operation earlier this summer, it leaves Saracens' Richard Wigglesworth in pole position to join Youngs at the World Cup.
Johnson must then decide whether to name a third scrum-half - Wasps' Joe Simpson - or maximise the versatility of a player like full-back Ben Foden, who has played Premiership rugby in the number nine position.
Care said on Twitter: "Absolutely devastated about my injury, but in the best hands for my op tomorrow.
"Wish the lads all the best to hopefully win the World Cup!!
"Thank you so much to everyone for your kind messages, helping me getting through this tough time. Supposedly everything happens for a reason?"
And Wigglesworth was one of the first to offer his condolences to Care, tweeting: "Gutted for Danny. Spoke to him yesterday. Worst timing possible. Big loss to the squad as a player and a person."
Care is the first player to be sidelined from Johnson's squad selection plans for a tournament that England kick off against Argentina in Dunedin on September 10.
Johnson said: "We are all hugely disappointed for Danny, who has worked extremely hard and has been an important part of the squad throughout our Rugby World Cup preparations.
"He featured in both warm-up fixtures (against Wales) and was on course for selection, so this injury is really disappointing for him personally and for us as a squad.
"Nobody wants to see a player ruled out at this stage through injury, and we all wish Danny a speedy recovery.
"In terms of our selection options we are fortunate to have depth at nine with Ben Youngs, now back into full training, Joe Simpson and Richard Wigglesworth.
"These guys have all been part of the Rugby World Cup camp and will be considered ahead of the final 30-man squad announced on Monday."
Care was the form scrum-half in England at the end of last season, and he had mounted a strong case to reclaim the England nine shirt from Youngs.
Wigglesworth, who enjoyed an impressive season with Aviva Premiership champions Saracens, started last Saturday's game in Cardiff but was replaced after 30 minutes, having suffered a blow to the head.
Care featured off the bench as a result, and he was arguably the shining light in an otherwise ineffective performance littered with wasted chances after England enjoyed set-piece supremacy.
England's final World Cup warm-up fixture is against Ireland in Dublin on Saturday week, scene of a 24-8 defeat in March that ended their Six Nations Grand Slam hopes, although the title was still secured.
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Gilbert Blitz 8S rugby cleat is a great cleat at a great price of $69.99. Get a new pair of cleats today.
A cool looking all black rugby cleat with the high performance adidas is known for. Get in the Gear!
Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
The All Blacks Performance t-shirt is black with hints of blue from the training jersey. Very Cool.
The New Zealand All Blacks training jersey for 2013/14. Get in the Gear!
The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.