Queensland went into day two of their clash at Bellerive Oval on Sunday needing a big total after slumping to 3-48 on day one.
But chasing Tasmania's 198 to claim first-innings points, the Bulls were knocked over for just 178, while the second-placed South Australia hammered 305 runs and claimed five wickets against Victoria.
The competition rewards bonus points to teams that score more than 200 runs, and for every wicket a side takes during the first 100 overs of the first innings, respectively.
South Australia's efforts and Queensland's batting capitulation mean the Bulls can no longer make up the points difference needed, even if they win outright.
It also denies retired Test opener Khawaja a final game for Queensland after the 39-year-old confirmed he would hang up his boots from first-class cricket at the end of the season.
Khawaja didn't take to the field on Sunday, as he awaits the birth of his third child.
Despite Sunday's disappointment, Khawaja has tasted success in the domestic four-day competition. He captained Queensland to claim the 2021 Shield final, when the Bulls crushed NSW by an innings and 33 runs in Brisbane, on the back of a brilliant 192 from Marnus Labuschagne.
On Sunday, Jack Clayton (37 runs off 84 balls) and Lachlan Hearne (48 runs off 88 deliveries) provided a glimmer of hope for Queensland with a 49-run partnership, but after Clayton fell the Bulls lost 5-70.
Having taken the prized scalps of Hugo Burden and Labuschagne on day one, Lawrence Neil-Smith (4-49) shone with the ball again, grabbing both Clayton and Hearne.
Australia's short-form spinner Matt Kuhnemann took 3-14, including a classy caught-and-bowled to dismiss Hayden Kerr for a duck.
Tasmania finished the day leading by 153 runs, having reached 5-133 in their second innings.
The home side got off to a rocky start, with Xavier Bartlett and Michael Neser reducing Tasmania to 3-10, after the loss of Caleb Jewell (first-ball duck), Tim Ward (4) and Charlie Wakim (0).
Test opener Jake Weatherald (62 runs from 57 balls) settled the Tigers' nerves, before Jordan Silk chipped in with an unbeaten 49 off 122 deliveries.
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