Although trailed by leaks to the Australian media, Toomua's selection for Saturday's match at Sydney's Olympic stadium is a sensational reversal by McKenzie, who had been Cooper's main cheerleader after he was dropped by previous coach Robbie Deans.
"Quade was disappointed, as was every player not picked," McKenzie told a news conference.
"That's the way it is, that's the nature of the business. We've picked the guys who are doing what we want and are best-suited to what we want to do."
Toomua was one of five uncapped players from the ACT Brumbies in the matchday 23 but the only one to start, with scrumhalf Nic White, centre Tevita Kuridrani, versatile lock/loose forward Scott Fardy and prop Scott Sio all on the bench.
"It's performance orientated, the Brumbies have been playing great football all season," McKenzie added. "The guys in form, the guys that are doing well, are the guys we've picked."
The former Queensland Reds coach said he had no qualms about blooding so many uncapped players in a test against the world champions.
"When's the right time to debut? I don't know," he said. "You just pick guys when they're ready and when you need them."
Hugh McMeniman was also included in the side at blindside flanker, earning a recall to win his 22nd cap after nearly five years in the international wilderness.
"I'm just really excited to be back in the Wallabies squad," said McMeniman. "There's a lot of different guys now but they're a really enthusiastic bunch of guys."
The selection of Jesse Mogg at fullback, one of six Brumbies in the starting line-up and 10 in the squad, could be an indication of the way the Wallabies will play.
"He's got moments of brilliance in him," said McKenzie. "He's a very good attacking player."
(Reporting by Nick Mulvenney, editing by Peter Rutherford)
