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Prop Andrew Sheridan has missed out with a neck injury but New Zealand-born inside centre Riki Flutey has recovered from a hamstring problem to line up against the All Blacks.
Johnson had promised there would be no sweeping changes to the side crushed 42-6 by the Springboks last weekend - but the decision to replace Cipriani with Flood was not unexpected.
Cipriani recovered from a gruesome dislocated fracture of the ankle six weeks early in order to play for England this autumn but he has failed to live up to the huge expectations.
The 21-year-old awarded himself just five out of 10 for his performance in the win over the Pacific Islands before struggling technically and tactically against both Australia and the Springboks.
Cipriani has had two kicks charged down this autumn that have led directly to tries - against the Pacific Islanders and South Africa - and there remain concerns over his defence.
Flood’s last England start came against the All Blacks in the second Test of the summer tour to New Zealand.
The decision to replace Rees with Lipman came as a surprise given the Wasps flanker was one of the England players to have impressed against the Wallabies and Springboks.
Kennedy will win his second Test cap in place of Palmer, who suffered a calf injury against the Springboks.
Johnson has opted to changed the balance of England’s replacement bench to four forwards and three backs, opening the way for Leicester’s Dan Hipkiss to return to squad.
England team: D Armitage (London Irish); P Sackey (Wasps), J Noon (Newcastle), R Flutey (Wasps), U Monye (Harlequins); T Flood (Leicester), D Care (Harlequins); T Payne (Wasps), L Mears (Bath), P Vickery (Wasps), S Borthwick (Saracens, capt), N Kennedy (London Irish), J Haskell (Wasps), M Lipman (Bath), N Easter (Harlequins).
Replacements: D Hartley (Northampton), M Stevens (Bath), T Croft (Leicester), T Rees (Wasps), H Ellis (Leicester), D Cipriani (Wasps), D Hipkiss (Leicester).