Warner blasted a dynamic 139 from 126 balls, but NSW suffered an embarrassing collapse around him.
They lost their last seven wickets for 39 runs and 6-30 after Warner spooned one to long on, to be all out for a below par 253.
The capitulation gifted Queensland a comfortable run chase, which they achieved with six overs remaining.
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Usman Khawaja (63 from 52) continued to do everything in his power to fight his way back into the mix for a Test return, scoring his third consecutive half century for the Bulls.
Warner was dropped from the Australian one-day side for poor form and started the domestic Cup competition with scores of 4, 0 and 17.
But with the pressure building, Warner responded in style, belting 13 fours and six massive sixes.
Warner is always one to back his ability, and he has scored five half centuries from his past 10 Tests - more than any other player.
But his jubilant reaction upon bringing up three figures from 96 balls suggested the innings meant a lot.
It was a timely reminder to selectors about his capabilities at the top of the order, but it was captain Steve Smith, run out for 4, who had to deliver the verbal message.
"He played pretty well. A bit slow early on but he struck the ball nicely today," Smith said.
"He was pretty happy with the way he hit them. Hopefully he can go off in the next couple of games as well."
Warner will certainly need to.
The loss means the Blues will most likely need to win their last two matches to make the one-day Cup preliminary final.
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Queensland openers Khawaja and James Peirson (52) put on 118 to set the platform, before middle-order batsmen Chris Lynn (78 not out) and Jason Floros (38) saw the Bulls home for their third win of the tournament and up into second place on the table with a bonus point in their favour.
The Bulls' were up against the ropes with Warner taking advantage of every corner of the tiny North Sydney Oval to hit boundaries.
But led by captain and man-of-the-match James Hopes (4-38), Queensland stuck to their guns and eventually NSW went to water, despite some tidy bowling from Nathan Lyon (2-38).
"At one stage we thought they could go close to 400 the way they were going. Davey was on fire," said Khawaja.
"But it was a massive wicket when we got Davey out. Hopesy bowled beautifully at the end there."