The New Zealand-born full-back was included in head coach Andy Robinson's training squad in September immediately after qualifying to play for England on residency grounds.
But his form has since dipped and error-strewn displays for Wasps against Sale, Edinburgh and Toulouse have proven costly.
Van Gisbergen's Wasps colleague Josh Lewsey has been preferred at full-back as Northampton winger Ben Cohen wins a recall to the side.
Cohen has not started a Test since Robinson took over from Sir Clive Woodward and was left out of the September training squad.
But Cohen responded to his omission with six tries in four games for Northampton and will win his first cap since appearing off the bench against France in February.
With Van Gisbergen on the bench, fly-half Charlie Hodgson retains the goal-kicking responsibilities but England will have no recognised on-field back-up.
England's World Cup-winning centre Mike Tindall returns to the side after missing the Six Nations through injury and will be partnered in midfield by Newcastle's Jamie Noon.
In the pack, Worcester's Pat Sanderson will win his first cap since 2001 and has been listed as blindside flanker in the absence of the injured Joe Worsley (knee) with Lewis Moody starting in the seven jersey.
Sanderson's previous caps have all come as part of a second string England side - the 1998 tour and the 2001 Churchill Cup - but his performances as captain of a belligerent Worcester side has earned him a start against the Wallabies.
With Simon Shaw (back) and Alex Brown (neck) out injured, experienced Bath pair Danny Grewcock and Steve Borthwick start in the second row.
Van Gisbergen, Lee Mears, the Bath hooker, and Leicester lock Louis Deacon complete an uncapped trio on a bench that also includes centre Olly Barkley, scrum-half Harry Ellis, loose-forward Chris Jones and prop Matt Stevens.
England have lost four of their eight Tests under Robinson and the only Red Rose victory over a leading nation in the last year came against South Africa last November.
When Robinson announced his 22-man squad for the Wallabies match last Thursday he defended Van Gisbergen's drop in form.
"I have no doubts about Mark Van Gisbergen," Robinson insisted.
"All players go through difficult patches. I have been pleased with what I have seen of Mark and the way he has worked and how he has fitted in here with England.
"I have really enjoyed having him in the squad."
The England team to play Australia on November 12 at Twickenham: J Lewsey (Wasps); M Cueto (Sale), J Noon (Newcastle), M Tindall (Gloucester), B Cohen (Northampton); C Hodgson (Sale), M Dawson (Wasps); A Sheridan (Sale), S Thompson (Northampton), P Vickery (Gloucester), S Borthwick (Bath), D Grewcock (Bath), P Sanderson (Worcester), L Moody (Leicester), M Corry (Leicester, capt).
Replacements: L Mears (Bath), M Stevens (Bath), L Deacon (Leicester), C Jones (Sale), H Ellis (Leicester), O Barkley (Bath), M Van Gisbergen (Wasps).