Winger Mark Gerrard is a surprise late inclusion, but Mortlock is still suffering the lingering effects of a head knock he received against the Chiefs last weekend and the blockbusting Wallabies centre was ruled out of the side as a precautionary measure.
Mortlock's absence sees Adam Ashley-Cooper move from the wing to outside centre and paves the way for new recruit Peter Playford to make his Super 14 debut on the left wing.
Lock Alister Campbell will take over the captaincy duties with Gerrard coming onto the bench.
"It's always disappointing to lose a quality player like Stirlo (Mortlock)," Brumbies head coach Laurie Fisher said.
"He's still suffering a few effects from his head knock and it just wasn't worth risking him. But in saying that, Coopy (Ashley-Cooper) showed some excellent form for us at 13 during the trials.
"He's a powerful ball runner and defended at inside centre last week against the Chiefs, so we're confident he'll get the job done for us on Saturday night."
Gerrard, meanwhile, trained well enough on Thursday and Friday to convince the coaching and medical staff he is fit, despite reports initially leaning towards a grade-two tear in his medial knee ligament.
Gerrard was not able to walk on Sunday and his recovery was jokingly described as 'Lazarus-like' by team-mates.
He said: "I expected the worst when it happened on Saturday afternoon in Hamilton, but to be able to run three days later, I'm very happy about it.
"So I've just to do everything right before the game to get it better.
"A couple of days preparation before playing is probably not ideal for a game but I'm happy where I am."
Gerrard said the loss of Mortlock was a factor when deciding whether or not he would play, but he had no doubts with the decision.
"With Stirlo having the head knock, Laurie asked 'would you be able to play?' and I ran as best I could with it on Wednesday on it and it felt fantastic," Gerrard said.
"I'm not worried about how I'll feel playing tomorrow [Saturday]."