Khawaja took full toll of a controversial decision early in his innings and was finally dismissed for 127 late on Thursday at Bellerive.
Queensland were well-placed at stumps on 6-309, although the home side fought back with three late wickets.
While Queensland are second-last on the Shield ladder and Tasmania are bottom, either side could still be in contention for the final against SA if they have a big win.
Tasmania won the toss and threatened several times to break through the Queensland top order, but Khawaja batted superbly for his 43rd first-class hundred. It is his first Shield ton since November 2023.
He also survived a massive shout from the Tasmanians when he appeared to edge opening bowler Gabe Bell to keeper Jake Doran.
Khawaja had only made 11 and the home side was aghast when Shawn Craig ruled not out.
The century from 221 balls, with 12 fours and a six, continued the 38-year-old's form upswing after a tough domestic Test series against India.
He only managed one half-century in the Border-Gavaskar series.
But Khawaja rebounded to post his highest Test score of 232 in Sri Lanka in late January. That solidified his spot ahead of the June Test championship final against South Africa at Lord's and next summer's domestic Ashes series.
"It was pretty tough, pretty much the whole time. It's quite green and pretty soft, but it was good to bat with Uzzy - he's awesome to bat with," said teammate Lachlan Hearne.
"It was good fun out there."
Khawaja and Hearne put on 110 for the fourth wicket, before Bell gained some revenge when he had the opener caught by Beau Webster at second slip.
Hearne made 74, his highest first-class score, but a century went begging when he was run out on a quick single that wasn't there.
Kieran Elliott's outstanding throw from side-on was a direct hit.
Jimmy Peirson was also dismissed in the last over, leaving Michael Neser and Jake Wildermuth the not out batsmen. They will aim to take the score past 350 on Friday.
"It was a bit annoying, me personally getting run out there and Jimmy at the end. But six for 300, we'd probably take that at the start of the day," Hearne said.
Webster claimed 3-54 from 19 overs and was the only multiple wicket taker.
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