The 23-year-old held the innings together to finish unbeaten on 87 as the Bulls reached 5-235 to pass the target with under an hour remaining and further rain threatening.
The result ends a three-match winless run for Queensland and pushes them to equal second, albeit narrowly adrift of Victoria who have collected more bonus points.
With two rounds remaining, NSW are out of contention with the result equalling the state's worst winless run (nine matches).
Queensland were on the edge at 3-43 in pursuit of 233 before Clayton and Max Bryant (28) combined for a 52-run stand.
But an 86-run partnership between Clayton and Jack Wildermuth (38) proved pivotal.
"We knew that if we could get two good partnerships going we could go a long way towards winning the game," Clayton said.
"It wasn't my most fluent innings by any stretch of the imagination, but I just tried to stick to my process, have a plan and take it as deep as we could and put the pressure back on New South Wales."
Clayton, with just one century in his ten previous Shield matches, has been a fourth-day specialist of late having played a match-saving innings against high-flying Western Australia in December.
Clayton was rarely troubled as the ball got old but he did survive one massive lbw appeal off NSW paceman Chris Tremain.
Queensland suffered a hefty 164-run loss just last week in Melbourne.
"Coming off the last game against Victoria, when the ball was nipping around we weren't proactive in taking the game on, and I think that is something we did a lot better in this game," Clayton added.
The day started perfectly for NSW who knocked over former Test opener Joe Burns in the first over for 12.
Seamer Sean Abbott (2-75) and allrounder Hayden Kerr (2-37) were the key wicket-takers for the Blues.
Defeat leaves their record at four defeats and four draws this season, and ensures that their slim hopes of reaching the Shield final are over.
"I think we were about 60 runs short in the end and poor sessions with the bat cost us," NSW captain Kurtis Patterson said.
"There was a lot of optimism going into today especially with getting early wickets, and especially Joe (Burns) given his experience.
"The wicket played quite well and stayed pretty true all day.
"Losing key moments has cost us and that has been the story of our year really."
8°C