The combative left-hander, who scored an emotional 145 in the first innings, added another 102 to help fire Australia to a 363-run lead at a sun-drenched Adelaide Oval.
Steven Smith added a half-century to his own first innings ton to push the hosts to 290-5. He was unbeaten on 52 at stumps, with wicketkeeper Brad Haddin on 14, and Australia in position to make an early declaration on the final day.
Warner gazed at the sky in tribute to batsman Phillip Hughes during his first innings knock and repeated the gesture on Friday after raising his sixth hundred in his last 11 Test innings.
He got himself out attempting a frivolous reverse sweep and was bowled by legspinner Karn Sharma as the Australians picked up the tempo in the last session.
Mitchell Marsh joined in the party, smashing 24 runs, including three sixes, off one over from Sharma. But Marsh chanced his arm one time too many and was caught slogging in the deep after a cavalier 40 off 26 balls.
Injured captain Michael Clarke could not repeat his first innings heroics when he scored 128 despite a painful back strain and was caught behind for seven off the bowling of Varun Aaron.