After rain delayed the start of the third day's play for more than two hours, England staggered to lunch at 36 for four, still 380 runs behind Australia's 416 for eight declared.
Ben Stokes was yet to score and Jonny Bairstow had come into bat.
Boland, who can do no wrong, claimed two wickets in his first 19 balls, highlighted by the dismissal of Root, who yet again dabbled outside off-stump and speared a high two-handed catch to Steve Smith at second slip.
Boland has now taken nine wickets in the series at just 6.11.
England are now playing only for their Ashes pride after going down by an innings and 14 runs inside three days in Melbourne to give Australia a 3-0 lead with two Tests to complete.
The Australians removed both openers with Mitchell Starc taking his series tally to 15 wickets.
Haseeb Hameed was dropped on two in a diving one-handed chance by wicketkeeper Alex Carey but Starc got him in his next over.
Hameed attempted to drive, only for Starc to clatter his middle-stump for six with a beautiful delivery.
It continued a depressing run of outs by the England openers with stands of 0, 23, 7, 4, 4, 7 and 22.
Crawley on seven gave a tough chance to Marcus Harris at short leg off Australian skipper Pat Cummins, flicking off his pad and Harris getting one hand to it but unable to take the catch at the second attempt.
Crawley was enjoying a charmed life after a massive reprieve before he had scored late on day two when he was caught by David Warner at slip, only for Starc to be no-balled for over-stepping.
But he finally fell for 18 in Boland's second over.