Prop Jenkins takes over from his Cardiff Blues colleague Sam Warburton, who is serving a three-week ban after he was sent off during Wales' agonising semi-final loss to France three days ago.
Toby Faletau will make his seventh start of the tournament - the only Wales player with a 100% appearance record - but he moves from number eight to openside flanker as Warburton's replacement.
Former Wales skipper Ryan Jones will fill the number eight role, with Paul James packing down at tighthead prop instead of Adam Jones, who has a calf muscle injury.
One change, also in the pack, sees Bradley Davies replacing Alun-Wyn Jones. Ospreys lock Jones is on the bench, where forwards Ryan Bevington and Andy Powell have been handed call-ups.
Jenkins, capped 81 times, has led Wales on two previous occasions. He replaces Warburton, who cannot play again until November 7.
Warburton, one of the tournament's most influential players, received a red card from Irish referee Alain Rolland for what was deemed a dangerous tip tackle on France wing Vincent Clerc.
It happened just 18 minutes into the contest - Wales had already lost an injured Jones - and left them having to play for more than an hour with 14 men.
But despite that disadvantage, they were ultimately only edged out 9-8 and scored the game's solitary try through scrum-half Mike Phillips.
Wales team to play Australia: L Halfpenny (Cardiff Blues); G North (Scarlets), J Davies (Scarlets), J Roberts (Cardiff Blues), S Williams (Ospreys); J Hook (Perpignan), M Phillips (Bayonne); G Jenkins (Cardiff Blues, capt), H Bennett (Ospreys), P James (Ospreys), B Davies (Cardiff Blues), L Charteris (Newport Gwent Dragons), D Lydiate (Newport Gwent Dragons), T Faletau (Newport Gwent Dragons), R Jones (Ospreys).
Replacements: L Burns (Newport Gwent Dragons), R Bevington (Ospreys), A-W Jones (Ospreys), A Powell (Sale Sharks), L Williams (Cardiff Blues), S Jones (Scarlets), S Williams (Scarlets).
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