Australia hold an overall lead of 257 at the WACA Ground.
Chris Rogers (42 not out) played a strong supporting role to Warner, who crunched 13 fours and one six from 94 deliveries in his unbeaten 81.
It has been a shocking day for England, who will have to hand back the urn if they go three-nil down in the series with a defeat in Perth.
England took the field for Australia's second innings without pace spearhead Stuart Broad, who suffered a foot injury while batting in the morning session.
While Broad was having x-rays done, England fumbled chances to dismiss both openers.
Warner began Australia's second innings in a hasty manner, aiming several big swings at Tim Bresnan's bowling in the second over of the innings before getting off the mark with a lusty cut.
Wicketkeeper Matt Prior made a couple of costly errors, missing a stumping when Warner was on 13 and failing to move for a catch when Rogers was on 26.
Alastair Cook at first slip lunged late and dropped the chance off Jimmy Anderson's bowling.
The home side's pace attack exploited the cracks in the WACA pitch to mess with England's heads and bowl the tourists out for 251 before lunch on Sunday.
England had resumed on 4-180 and lost 6-51 in the morning session in reply to Australia's 385.
Ryan Harris (3-48) and Peter Siddle (3-36) took three wickets each and complemented the brutal pace assault from left-armer Mitchell Johnson (2-62).
England's hopes rested on star No.5 batsman Ian Bell (15), who was out on review to Harris whose initial lbw appeal had been turned down.
Home-town hero Johnson had the crowd on edge after hitting a crack and causing wicketkeeper Brad Haddin to dive in front of first slip as Matt Prior took a bye in the 74th over.
Two balls later, Ben Stokes (18) pushed forward tentatively and was caught behind off Johnson at 6-198.
Tailenders Bresnan (21) and Graeme Swann (19 not out) scored some handy runs late in the innings.
AUSTRALIA FIRST INNINGS 385
ENGLAND FIRST INNINGS 251
AUSTRALIA SECOND INNINGS
C ROGERS not out 42 129 110 6 0
D WARNER not out 81 129 94 13 1
No wickets for 123
Bowling: J Anderson 8-2-29-0, T Bresnan 6-0-33-0, B Stokes 6-0-29-0, G Swann 13-5-31-0, J Root 1-0-1-0.
Batting time: 129 mins. Overs: 34.
Umpires: Billy Bowden (NZL), Marais Erasmus (RSA).