Rees, the 2009 Lions hooker, replaces fellow Scarlet Ken Owens to recreate the front row that battled the Springboks on tour three years ago. Owens misses out altogether, with Ospreys hooker Richard Hibbard providing the front row cover on the bench alongside his former regional colleague, prop Paul James.
(Alun Wyn) Jones, who captained the Wales XV to a 25-15 victory over the ACT Brumbies in their midweek fixture on Tuesday night, replaces Dragons lock Luke Charteris in the second row, with Charteris moving to the bench.
In the back row (Ryan) Jones comes in at No8 in place of injured Dragons flanker Toby Faletau, who returned to Wales from Canberra on Tuesday after breaking a bone in his hand.
Beck, who also featured prominently in the midweek clash with Brumbies, comes into the starting line-up in place of Scarlets centre Scott Williams. Williams joins Ospreys scrum-half Rhys Webb and Perpignan pivot James Hook in providing cover from the replacements bench for the backs.
Elsewhere, Ospreys flanker Justin Tipuric offers back row cover from the bench to complete the matchday line-up.
"After the first Test Australia are obviously in the ascendency, but the tour is not over by any means and we have all to play for on Saturday," said 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."
Dragons wing Aled Brew will return home this week after a hip contusion (bruise) has ruled him out of contention for selection for the next two weeks, although no further players will be added to the squad.
Wales: Leigh Halfpenny; Alex Cuthbert, Jonathan Davies, Ashley Beck, George North; Rhys Priestland, Mike Phillips; Gethin Jenkins, Matthew Rees, Adam Jones, Bradley Davies, Alun Wyn Jones, Dan Lydiate, Sam Warburton (Captain), Ryan Jones
Replacements: Richard Hibbard, Paul James, Luke Charteris, Justin Tipuric, Rhys Webb, James Hook, Scott Williams
NB Bold denotes Lion