Johnson, who himself toured three times with the Lions and skippered the squad twice, is without 11 of his original Elite Player Squad, with seven 2009 Lions among them.
Harry Ellis, Riki Flutey, Lee Mears, Andrew Sheridan and Phil Vickery are all out injured, while the Wasps duo of Simon Shaw and Joe Worsley have both only just returned to domestic action following lengthy lay-offs.
Having started both the first and third Tests against South Africa on the wing, Monye switches to full back for the Twickenham clash with the Wallabies, with Cueto given a wing berth along with Bath's Matt Banahan.
Croft and Moody start in an all-Leicester backrow that also sees Jordan Crane make his first Test start at No8.
Wilkinson, who was unable to press his claims for a full house of Lions tours as a result of a knee injury he suffered last September, is set for his England comeback following 18 months away from the international fold.
Fellow World Cup winner Steve Thompson returns at hooker for the first time since 2006, with the Brive No2 having reversed his decision to retire from the sport after receiving a second opinion on a neck injury.
Dan Hipkiss and Shane Geraghty form a new-look centre partnership, Louis Deacon joisn skipper Steve Borthwick in the second row and David Wilson covers for the absent Vickery and Julian White at tighthead prop.
Uncapped Northampton lock Courtney Lawes is among the replacements, as is former Wasps and Leicester centre Ayoola Erinle who is now plying his trade with Biarritz.
England vs Australia, Saturday, November 7
U Monye (Harlequins); M Cueto (Sale Sharks), D Hipkiss (Leicester), S Geraghty (Northampton), M Banahan (Bath); J Wilkinson (Toulon), D Care (Harlequins); T Payne (Wasps), S Thompson (Brive), D Wilson (Bath), L Deacon (Leicester), S Borthwick (Saracens, capt), T Croft (Leicester), L Moody (Leicester), J Crane (Leicester).
Replacements: D Hartley (Northampton), D Bell (Bath), C Lawes (Northampton), J Haskell (Stade Francais), P Hodgson (London Irish), A Goode (Brive), A Erinle (Biarritz)
Denotes Lions tourist