After dismissing the outgunned tourists for 271 and a 280-run first innings lead, skipper Steve Smith did not enforce the follow-on, preferring to recharge his bowlers and bat a second time.
By close on the third day, Smith had led the Australians to 179 for three with his virtuoso unbeaten knock of 70 off 70 balls with the under-used Mitchell Marsh, elevated to fifth in the order, chipping in with 18.
Australia crushed the Windies by an innings and 212 runs in the first Test in Hobart and have lost only 10 wickets for 1,313 runs in three incomplete innings.
Smith had Sunday's third Test in Sydney and the extra bowling workload in mind when he decided not to put the Windies back in to bat.
The Australians went about chasing quick runs and lost wickets along the way.
Both openers were gone by the 11th over as the Windies bowlers enjoyed their best spells of the series.
Debutant Carlos Brathwaite followed up with the prized wicket of David Warner.
Warner attempted to steer a lifter behind the wicket only to be well caught by Holder in the gully to miss out again with 17 following his 28 in the first dig.
First-innings centurion Usman Khawaja played some improvised shotmaking for his breezy 56 off 61 balls before he was caught behind attempting to paddle Holder behind the wicket.
But despite their dire position the Windies showed more resolve against the odds on the third day.
resistance in the last over before tea, getting Bravo caught in the gully to finish with four for 72.
Off-spinner Nathan Lyon collected four for 66 and now has 179 career Test wickets.
It was the Windies' highest innings score in a Test at the Melbourne Cricket Ground since 1988 as they kept the dominant Australians in the field for 100.3 overs.
Bravo was in sight of his second century of the series after his 108 in Hobart, before he fell short slicing Pattinson to Smith in the gully.
He faced 204 balls and hit eight fours in a disciplined innings that his team badly needed after tumbling to 83 for six.
Carlos Brathwaite's luck ran out when he spooned a high return catch back to Lyon in the final over before lunch, ending a dogged 90-run stand with Bravo.
Brathwaite was earlier given out twice only to be recalled both times for a front-foot no-ball by paceman Pattinson.
Brathwaite swung lustily on 13 and had his stumps scattered by Pattinson before an umpire's check detected a no-ball.
The Barbados all-rounder was again recalled on 50 after he was caught at fine leg only for replays to pick up another Pattinson no-ball.
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