Jones will come in at number eight in place of Toby Faletau, who returned home yesterday [Wednesday] after breaking a bone in his hand in the 27-19 first Test defeat in Brisbane.
Alun Wyn Jones replaces lock Luke Charteris, hooker Matthew Rees comes in for Ken Owens and Ashley Beck will make his first start at centre in place of Scott Williams.
Charteris and Williams, who needed stitches to a mouth wound midway through the second half on Saturday, both drop down to the bench.
George North is expected to make a recovery from the dead leg that forced him off after 31 minutes at the Suncorp Stadium.
Wales claimed a morale-boosting 25-15 success in their tour match against Super Rugby franchise Brumbies, and will be looking to take that momentum into the Etihad Stadium as they bid to level the three-match series.
"After the first Test Australia are obviously in the ascendancy, but the tour is not over by any means and we have all to play for on Saturday," said Wales caretaker head coach Rob Howley.
"We are bringing three very experienced players into the pack, all three made an impact from the bench during the first Test which has justified their selection in the starting line-up this weekend.
"We were also impressed with the performances of Ashley Beck, Justin Tipuric, Richard Hibbard and Rhys Webb on Tuesday night and they have each very much played themselves into the squad.
"Having played two matches now on Australian soil we have acclimatised and are ready for another huge challenge this Saturday in Melbourne."
Wales have also confirmed Aled Brew will return home, with a hip injury ruling the wing out of contention for the next fortnight.
Wales squad for the second Test against Australia: L Halfpenny; A Cuthbert, J Davies, A Beck, G North; R Priestland, M Phillips; G Jenkins, M Rees, A Jones, B Davies, AW Jones, D Lydiate, S Warburton (Captain), R Jones
Replacements: R Hibbard, P James, L Charteris, J Tipuric, R Webb, J Hook, S Williams