Labuschagne and Khawaja came together after Warner fell to young pacer Jaden Seales, and barely put a foot wrong.
He was hit hard for nearly seven years in the opening session of the First Test between the two sides, reaching 72–1 at lunch.
But after the break with Labuschagne, he accelerated and took three off Jason Holder to complete his 50.
A faultless Khawaja, who has been a rock in the top-order this year, soon hit spinner Roston Chase for a four and then singled to reach his 18th half-century in his 52nd Test.
Khawaja had scored four Test hundreds and reached the 90s twice in the last 12 months, with more glory.