The England skipper spent time in hospital on the morning of the fifth day being treated for the effects of a viral gastroenteritis bug which had left him dehydrated.
And while he was able to resume his innings after the fall of the first wicket, his replacement Moeen Ali, having finished unbeaten on 42, he was not fit to return after lunch.
In obvious discomfort, Root battled to 58 at lunch but suffered a recurrence of symptoms during the session break.
“Joe was feeling exhausted at the lunch break and is resting up in the dressing room,” said a spokesman for the team. “He is feeling unwell and some of his symptoms have returned.”
England folded quickly after Bairstow was sent packing lbw for 38 with the last three wickets falling for 36, all out for 180.
Defeat by an innings and 123 runs completed a series of routs with only a draw in Melbroune on a pitch described as “poor” by the ICC saving the whitewash.
England had resumed on 93-4 but the loss of Moeen for 13, falling to Nathan Lyon for the seventh time in nine innings this series, started the rot.
When Bairstow followed him and Root did not return after lunch the end came quickly. and Root was also unable to come out for the presentation.
And Australia took one final chance to mock England at the ceremony with a back-drop cutout with two hands, one with the English flag and one with the Australian flag, and the latter held up four fingers in reference to the hosts winning the series 4-0.