Khawaja stepped up from his scratchy batting in Brisbane with a half-century as the tourists claimed the wickets of Cameron Bancroft and David Warner after surprisingly sending the Australians into the bat after winning the toss.
At the dinner break in the first-ever Ashes day-night Test, Australia were 138 for two with Khawaja on 53 and skipper Steve Smith unbeaten on 25.
Smith, the bane of England's bowlers at the Gabba with his match-defining unbeaten 141, was soon engaged in a war of words with Stuart Broad as the tourists looked for a way to unsettle the imperious Australian skipper.
Khawaja had faced 26 balls and was settled in by the time Ali came on to bowl.
But he had a life on 44 when he top-edged a Chris Woakes bouncer to deep backward square where Mark Stoneman put down a two-handed chance.
Khawaja reached his ninth half-century in his 26th Test with a cut shot off Ali to the boundary.
Joe Root, who became the first England captain since Bob Willis in 1982 to bowl after winning the toss in Adelaide, failed to gain any reward until the 15th over after two rain stoppages.
Warner played Broad into the covers where Ali fumbled the ball as Bancroft set off for a run from the non-striker's end.
Woakes picked up the ball and hit the stumps from mid-off as Bancroft scrambled to make his ground and was run out in the mix-up for 10.
Woakes captured the prized wicket of David Warner for 47 in the 34th over.
Warner edged an outswinger to Jonny Bairstow and left the home side 86 for two as Smith came to the crease.
Fast bowlers James Anderson and Broad wasted the new pink ball by bowling short of a length in the important first hour.
Ashes holders England cannot afford another defeat after their 10-wicket first Test mauling at the Gabba.
The first-ever Ashes Test under lights has long been earmarked as England's best chance of a win in Australia given the extra swing and movement of the pink ball in twilight conditions.
Australia have beaten New Zealand and South Africa in the two day-night Tests played at the Adelaide Oval.
The hosts named the same team that won the first Test, while England gave Somerset seamer Craig Overton his Test debut in place of Jake Ball in their only change from Brisbane.
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