The back injury that scuppered Khawaja in the first Ashes Test also ruled the 38-year-old opener out of the big win in the second at the Gabba, where Australia took a 2-0 series lead.
Usual No.5 Travis Head continued replacing Khawaja next to second-gamer Jake Weatherald with impressive results.
Head, a centurion in Perth, took the shine off the new ball in Brisbane with fast starts of 33 and 22, while Weatherald made a breakout 72 in the first dig before falling to a pinpoint Jofra Archer yorker.
"'Weathers' has come in for the first time and the way he's gone about it as well has just set the tone at the top," Labuschagne said.
Australia have used seven different opening partnerships across 17 Tests since David Warner retired in early 2024, but Head and Weatherald have shown the makings of a settled pairing at the top.
In both Gabba knocks the pair laid a platform for those below to kick on, with the Aussies all out for 511 in the first dig and then rollicking home in the second to win by eight wickets.
Labuschagne has made two half-centuries this series in three knocks coming in after the new openers and felt they were making the middle and lower orders better.
"For the last three innings, we've got off to a bit of a flyer and you kind of get out there and that momentum sort of just rubs off," he said.
"It's been nice to come off the back of momentum and be able to put the bowlers under pressure from the start of my innings.
"I've really enjoyed that. But it's each game on its own, trying to read the conditions and read what the team needs."
Selectors are in for a dilemma with Khawaja a chance to be fit for the third Test that begins in Adelaide on the day before his 39th birthday.
Representing South Australia in the Sheffield Shield, Weatherald and Head both know Adelaide Oval intimately, with the latter scoring tons in his last three Test matches there.
Axing Khawaja now would make it hard to see a return to the Test team.
Labuschagne put faith in the selectors for the third Test after their bold call to drop Nathan Lyon for Michael Neser was vindicated in the pink-ball Test.
"They looked at the game objectively and said 'What's the best way for us to win this game with all the information we have on pink-ball cricket? What plays? What's favoured, is it spin or is it pace? What type of bowler?'," Labuschagne said.
"And they made the decision."
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