Pocock, arguably the most influential loose forward in the tournament, and fullback Folau, Australia's most potent attacking weapon over the last two years, failed fitness tests on Friday and were replaced by Ben McCalman and Kurtley Beale.
Cheika said he had never even considered risking Pocock, who has a calf strain, and Folau, who has an injury problem, despite their importance to the team.
"They couldn't do their jobs and that's the key," he told reporters on Saturday.
READ MORE
Your guide to Wallabies v Scotland
"You've got to be able to do your jobs in this team and I don't think either player could do it to their full potential."
With the loss of Pocock, Cheika has abandoned the deployment of two specialist openside flankers in his back row and brought Michael Hooper back from suspension to join stalwart blindside flanker Scott Fardy and the bulkier number eight McCalman.
Beale, who started the pool victory over Uruguay at fullback but has otherwise been used off the bench in this tournament, will win his 58th cap against the Scots at Twickenham.
"It's really just a straight swap for those guys," said Cheika.
"We'll just ask them to improve the team with what they bring. Both have already made contributions to the side in this tournament and I'm sure they'll continue to contribute in spades."
Cheika's aim since he took over as coach a year ago was to put together a playing system that squad players would be able to slot into when necessary.
"We've been working hard over the last 10, 11 months to get real depth in all positions," he said.
"I know Pocock and Folau are great players but I really believe in the guys who are coming into their positions. That's something we want to build on."
In the other change to the side, Rob Simmons comes into the second row for Dean Mumm to fix a lineout that struggled at times in the epic pool victory over Wales last week.
Simmons, who started the pool games against Fiji and England before losing his place for the Wales match, said the rivalry with Mumm had been good for both players.
"We've been pushing each other and we help each other out from week to week too, on how we’re going to run the lineout and things like that," the 26-year-old said.
"There's been a bit of competition and Cheik's selection has been keeping us on our toes."
