Meyer said his side needed freshening up after two physical wins over Argentina and the long trip from South America to Brisbane to take on the Wallabies, who lost their opening two encounters against New Zealand.
"There will be a few changes, mostly due to rotational, and also we want to have the most fresh as possible team on the field," Meyer told local reporters in Brisbane on Monday.
"We've travelled a lot ... and we're going to play three away matches on the trot and we have to travel for all three so it's important to have fresh guys."
The Springboks, three times winners of the Tri-nations before the introduction of Argentina last year, smashed the Pumas 73-13 in Johannesburg on the opening week before narrowly overcoming them 22-17 in Mendoza.
Meyer indicated that hooker Bismarck du Plessis was likely to start in place of Adriaan Strauss for the clash at Lang Park, where the Springboks have never won in seven attempts.
Turning to the Wallabies, Meyer said he felt Cooper was due to reclaim the number 10 shirt and re-unite with scrumhalf Will Genia, despite coach Ewen McKenzie using the mercurial playmaker off the bench and naming rookie Matt Toomua flyhalf in the two losses against the All Blacks.
"I think it's just a matter of time when (Cooper) comes back, just hopefully not against the Boks," the former Bulls coach said.
"A player like that I would love to have in my team.
"I just believe if Cooper plays well and Genia plays well then the Wallabies play well."
McKenzie, though, was full of praise for all of his flyhalf options.
"It's about how we want to play the game tactically, then we'll have a look at the best guys to do that," McKenzie said.
"We've got three playmakers (including Bernard Foley) in the group and I'm happy with all of them."
The former Queensland Reds coach hinted, however, that he could also make changes as he seeks his first win in charge.
"There's always the potential for change," the former prop added.
"We're playing a different team in a different context so different things will come into play so we're definitely looking at that.
"There's a clash of rugby approaches. They love having set-pieces and they structure most of their game from that. That's what they want. The question is whether you give it to them."