Khawaja hit a timely 87 for the Bulls on Thursday, as the hosts went to stumps at the Gabba on day three at 4-238 in reply to the Blues' 7(dec)-429.
In a match that appears destined for a draw, Matt Renshaw missed out on a chance to further press his Test claims on Thursday when bowled for 29, while Marnus Labuschagne was also out for five.
But there were at least positive signs for Khawaja, with the veteran's form looming as crucial for Australia this summer.
While all eyes have been on who will partner him at the top against England, Khawaja only averaged 15.37 in four Tests last winter.
The 38-year-old has had scores of 69, 46 and 0 in the Shield for Queensland, before looking in good touch at the Gabba.
"I've felt good all year," Khawaja said.
"I felt really good in that first game at AB Fields, that last game in Adelaide felt really good.
"I've felt really good the whole way through."
Khawaja said he was unsure if he would be made available for the Bulls' next match against Western Australia, making this innings potentially his last before the first Test on November 21.
He hit three boundaries in one over early from Ryan Hadley, while his shot of the day was a lovely drive down the ground off the quick later in his innings.
The left-hander also looked at his laconic best clipping Test teammate Nathan Lyon for two more boundaries through the legside, after sweeping the spinner for another.
But with a century in sight he fell in common fashion, edging a Charlie Stobo ball that was angled across his stumps and swung away.
Renshaw also gave himself the foundation to produce a score befitting his Test claims, before attempting to leave a Jack Edwards ball and edging it onto his stumps.
Australia's selectors will name an extended squad for the first Test in Perth after this Shield round, with Renshaw likely battling with Jake Weatherald for a spot in the group.
Whether either plays will likely depend on if Beau Webster and Cameron Green are both included in the XI, or if one makes way and a specialist opener is preferred.
Labuschagne looks certain to be there in Perth after a hot start to the summer, with the only question being if he is used as a makeshift opener or in his normal role of No.3.
He was out on Thursday when he glanced Hatcher straight to a short fine leg, before Hatcher also had Lachlan Hearne caught in the slips for nine.
But Jack Clayton's unbeaten 81 has all but killed off NSW's hopes of victory after a washed-out opening day.
The Blues would theoretically need to bowl Queensland out for under 280 on Friday, enforce the follow on, and then knock them over again.
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