Khawaja was unable to open in Australia's first innings in Perth on Friday after spending too long off the field dealing with back spasms.
The 38-year-old was cruelled again while fielding on Saturday, with his back injury flaring while jumping up at slip.
With Khawaja unable to bat, Travis Head was elevated to opener, and the South Australian cracked the equal sixth fastest century in Test history on the way to 123 off 83 balls.
Head's 69-ball ton wowed the 49,983 fans in attendance, and even had Khawaja appreciating the moment despite dealing with intense pain.
"He's not well,' Australia stand-in captain Steve Smith said of Khawaja.
"He's not moving particularly well in there, the old fella.
"But he just said before, it's probably one of the best back spasms he's ever had, given the circumstances of this fella (Head) right next to me."
Khawaja was heavily criticised for playing golf on Thursday, just a day out from the start of the Ashes.
But Smith dismissed suggestions the round of golf contributed to Khawaja's back injury.
"His preparation was the same as it's been for every Test match that he's played," Smith said.
"So yeah, there was nothing out of whack there by any stretch.
"Unfortunately, he just pulled up a bit lame early on in the game, and that happens when your back goes on you.
"I've been there myself when your back seizes up, and it's not a nice place to be. So I can feel his pain right now."
Khawaja made just two batting at No.4 in the first innings, meaning he has now failed to post a half-century in his past 11 Test innings.
The veteran's poor form - which included a dropped catch at slip on Saturday - and injury troubles means he could be in danger of losing his spot for the second Test at the Gabba, which begins on December 4.
Mitch Marsh and Josh Inglis would be among the contenders looking to earn a spot in the Test XI, while Australia could also replace Khawaja with Head at the top of the order, possibly opening the door for allrounder Beau Webster to return to the side.
Fans and experts have been quick to criticise Khawaja's decision to play golf the day before the start of the Ashes, but CA chief executive Todd Greenberg didn't have an issue with it.
"It (playing golf before a Test) has held him in good stead over the last couple of years. It's not uncommon for a lot of them to play golf a day prior," Greenberg told SEN.
"Did that correlate to any of the issues? I personally don't think so.
"I noticed Mitch Starc played golf with him, so it certainly didn't impact his performance (given he snared 7-58)."
FASTEST TEST CENTURIES
*54 balls - Brendon McCullum (NZ) v Australia in Christchurch, 2015/16
*56 balls - Viv Richards (WI) v England at St John's 1985/86
*56 balls - Misbah-ul-Haq (Pak) v Australia in Abu Dhabi 2014/15
*57 balls - Adam Gilchrist (Aus) v England at the WACA, 2006/07
*67 balls - Jack Gregory (Aus) v South Africa in Johannesburg 1921/22
*69 balls - Shivnarine Chanderpaul (WI) v Australia in Georgetown 2002/03
*69 balls - David Warner (Aus) v India at the WACA, 2011/12
*69 balls - Travis Head (Aus) v England at Perth Stadium, 2025/26.
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