Usman Khawaja's back injury has ruled the veteran opener out of the second Ashes Test and thrown his future in the Australian team further into doubt.

The 38-year-old's place in the XI had been under intense scrutiny since back spasms forced him from the field in the victorious first Test and left Travis Head to open the batting.

On Tuesday afternoon, Cricket Australia confirmed Khawaja was still battling the injury and would miss the day-night Test that begins in Brisbane on Thursday.

It means Head is set to continue partnering recent debutant Jake Weatherald at the top of the order, with Beau Webster and Josh Inglis the leading options to join the XI.

"(Khawaja) has put in a lot of work since the last game to try and get his body right but he hasn't come up, unfortunately," said Australian bowler Scott Boland.

Khawaja is remaining with the team to begin his rehabilitation and will race the clock to be fit for the third Test in Adelaide from December 17.

Even if he is able to recover, Khawaja is no guarantee to hold onto his spot for the remainder of the Ashes given a lean run of form and Head's heroics replacing him in Perth.

Khawaja nicked off after scoring just two in the middle order in his only dig at Optus Stadium, and will turn 39 during the Adelaide Test.

CA chief executive Todd Greenberg said late last month there was no correlation between Khawaja's back problem and his three days spent on the golf course leading up to the series opener.

Australia have opted against replacing Khawaja in the squad in a clear indication Head will shift from No.5 and open the batting.

Middle-order replacement option Webster has had an impressive first year as a Test cricketer, averaging 34.63 with the bat and taking eight wickets across seven matches.

He was the odd man out at the selection table for the first Test, with Cameron Green the only allrounder chosen in the XI that won by eight wickets.

Including Webster could mean pushing Green up to No.5, a spot he has filled just once in 33 Test matches.

Webster bowled extensively and batted in the nets at training on Tuesday night.

"(Webster) was making really good runs at six, he's bowled really important overs, you've seen him in the field, he's a gun catcher," Boland said.

"Any time he's in the team, it makes us a stronger team."

Inglis is the other option should Australia prefer a like-for-like replacement for Head, traditionally used as a middle-order aggressor in home conditions.

Inglis memorably smacked a century on Test debut in Sri Lanka earlier this year but has averaged a meagre 5.66 across his two Tests since.

On Tuesday night, Inglis spent significant time training in the slips cordon, where Khawaja usually fields.

Boland conceded the balance of the team had been disrupted "a little bit" by having to contend without Khawaja for at least the second Test.

But the gun paceman was confident in Australia's depth, having played all of his 15 Tests as a replacement for the so-called "big three" quicks.

"We probably planned to have Ussie there the whole time," Boland said.

"But I think the best thing about our team over the last few years is that when someone has come out due to form or an injury or something like that, someone's always stood up and done their job."