After rolling England for 172 in 32.5 overs at Perth Stadium on Friday, Australia were dealt a shock when told Khawaja wasn't allowed to open due to spending too long off the field at the end of the innings.
Khawaja had gone off twice due to back stiffness, with CA stating the 38-year-old suffered back spasms the second time he went off.
In the midst of England losing 5-12 in the space of three overs at the end of their innings, Australia skipper Steve Smith was seen motioning urgently for Khawaja to come back on.
Although Khawaja eventually re-entered the fray, the quick nature of England's demise meant he wasn't eligible to bat again until a few overs into Australia's innings.
Debutant opener Jake Weatherald was forced to face the first ball - something he hasn't done in his past 20 first-class innings - and he fell for a second-ball duck after being trapped LBW by a rampaging Jofra Archer.
Marnus Labuschagne, who was slated to bat at No.3 after Australia opted to select Weatherald as a specialist opener, was forced to open due to Khawaja's absence.
By the time Khawaja strolled to the crease in an unfamiliar No.4 spot, Australia were already in trouble at 2-28 following Labuschagne's departure for nine off 41 balls.
The initial confusion surrounding Khawaja's stint off the field led to a wave of criticism from experts and fans alike.
"They've obviously been caught off-guard, which is the last thing that Marnus wanted, the last thing that Jake wanted," former Test skipper Ricky Ponting told the Seven Network.
"Jake Weatherald would have forging a relationship with Usman all week to build up and face his first ball in Test cricket.
"That was all taken away."
Australian pace ace Mitchell Starc, who snared career-best figures of 7-58, described Khawaja's time off the field as unfortunate.
"He had a back spasm there the second time he came off, so we got caught off guard a little bit with the wickets falling pretty quickly the back end there," Starc said.
"It's just unfortunate that that was the case. He'll manage that overnight and see how we're at tomorrow."
The drama even caught England by surprise.
"I don't think we really even realised it," England paceman Brydon Carse said.
"You know, come the start of the innings, it was obviously probably more unsettling for the for the Aussies."
The day was much better for Australia's other debutant - speedster Brendan Doggett.
The 31-year-old bowled with good pace when he was first introduced in the 10th over, and he struck gold in his second spell when his bouncer to Harry Brook (52 off 61 balls) caught the danger man's glove.
Australia's muted appeals were initially turned down, but a convinced Steve Smith decided to review it after hearing Doggett say: "I didn't hear anything, but it moved."
Brook, knowing his fate, walked off instead of waiting for DRS to confirm the inevitable.
Amidst England's late collapse, another rising Doggett delivery struck tail-ender Carse flush on the helmet.
A rattled Carse departed a few balls later when he lofted Doggett into the deep for an easy catch.
Although Starc rightly deserved the plaudits for his masterclass display, Doggett walked off with the respectable figures of 2-27 in his first taste of Test cricket.
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