Opener Warner scored his first Ashes Test century and skipper Clarke raised his 25th Test ton and sixth against England as the Australians rammed home their 159-run innings lead to take firm control.
At tea, Australia had extended their overall lead to 458 runs at 299 for five with Test debutant George Bailey not out 33 and Brad Haddin on one.
England will already have to create Ashes history to win the Gabba Test with their previous highest winning fourth innings score at 332 for seven in Melbourne in 1928.
Clarke bounced back strongly from his first innings batting failure when he was caught off a Stuart Broad lifter for one and has now scored 1,029 runs at the Gabba at an average of 114.33.
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Warner raised his fourth Test ton with three runs off part-time spinner Joe Root a half-hour after lunch but later became another victim of Broad when he was caught behind for 124 off 154 balls with 13 fours and a six.
Clarke brought up his hundred just before tea with a two through the on-side off Root.
England's bowlers removed opener Chris Rogers (16) and number three Shane Watson (6) cheaply in the morning session.
Rogers was out to Broad's first ball of the day as he loftily cut to Michael Carberry at point.
Watson was pinned down by tight England bowling but went cheaply again in the match when he top-edged a pull shot off Chris Tremlett's third delivery high to Broad at mid-on.