Victoria went to stumps 6-136 on day three in their second innings at the Gabba for an overall lead of 163 runs after Queensland's bowlers, headed by former Australia U19 representative Jem Ryan (3-38), bowled with great control.
The Bulls resumed on Monday at 5-202, in reply to Victoria's 307 all out and were dismissed for 280.
Clayton added just five to his overnight 99 not out to continue a strong start to the season, that could not have come at a better time for a player pushing to be considered for Australia's faltering batting order.
Clayton, who has averaged 49.2 in his last 10 Shield innings, has also recorded strong first-innings scores of 82 and 67 previously this summer to take his season tally to 293 runs at an average of 73.25.
"Jack Clayton, who is a young guy that I played with, he's scored six centuries, averaging 38, and no one talks about him," Khawaja said on Kayo Sports during the second Test in South Africa.
"He's played 42 games now. When they devalue Sheffield Shield cricket, it frustrates me. If Marnus is good enough to play for Australia with that Sheffield Shield record (of averaging 38.91), why can't any of these other guys play?"
Clayton said he learned a lot from the retired Khawaja at the Bulls and valued his backing.
"I knew he thought I was a decent batter playing with him and he always tried to support me when he was here. I got a lot out of playing with him for four or five years," Clayton said.
"For him to publicly say that was obviously a nice thing to do and I am thankful."
Clayton, 27, said it had "always been a goal of mine" to play for Australia.
"My main focus is scoring runs for Queensland and that kind of stuff will take care of itself," he said.
"It was nice to get the hundred and put us in a good position in the game."
Victoria quick Matt Hennig claimed 4-54 on Shield debut, after impressing in his first List A match for the side last month against Tasmania.
Ryan, 22, then took to the bowling crease for the Bulls and had the visitors in early trouble.
Vics opener Sam Harper, fresh from being selected in the Australia T20 squad for the upcoming series against England, was out playing a T20-style shot.
Queensland set the trap and Harper slapped an upper cut to fly slip off Ryan to fall for six, after making an impressive 63 in his first dig.
Ryan has enjoyed a superb start to the Shield season, with 15 wickets in his three matches, and appears set for higher honours.
His Bulls teammate Cameron Gannon picked up 2-20 to go top of the wicket aggregate list with 18.
Victoria left-handers Campbell Kellaway and Oliver Peake top-scored in the second innings with 35 apiece.
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