Australia were 136 for six at tea on the fourth day, still needing a further 447 runs to reach their colossal victory target of 583.
No side has made more to win in the fourth innings of a Test than the West Indies' 418 for seven against Australia at St John's in 2002/03.
It seemed Australia might at least deny Ashes-holders England a wicket in Sunday's second session.
But shortly before tea, part-time off-spinner Root struck twice, with Yorkshire colleague Tim Bresnan also on target, as Australia lost three wickets for two runs in 23 deliveries.
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The 22-year-old, bowling from around the wicket, spun one outside Clarke's pads with the star batsman obligingly turning the ball to opposing captain Alastair Cook, who had just stationed himself at leg slip.
Clarke, missed on two, was out for 51, featuring seven fours, after putting on 98 for the fourth wicket with Khawaja, who shortly afterwards could do nothing but nick a sharply spun delivery to James Anderson at second slip.
Then seamer Bresnan had Steven Smith, off a thin inside edge, well held by diving wicketkeeper Matt Prior for one off what became the last ball before tea to leave Brad Haddin nought not out at the interval as a now sun-drenched capacity crowd caught their breath.