The 151-Test opener, resuming on an overnight 104, took his score to 134 off 244 balls at lunch with Jonny Bairstow on 16 and the tourists 264 for four.
It is Cook's 32nd Test century and his first Ashes ton for almost seven years, and follows an underwhelming six previous innings in this series.
At 3-0 down after three Tests, the Ashes urn is already lost to Australia, but England are chasing a face-saving win in the showpiece Boxing Day Test.
Root yet again failed to convert his half-century into a big score when he top-edged a hook shot off Pat Cummins to Nathan Lyon at deep square leg.
The England captain reached his third half-century of the series early on day three but was clearly furious with himself when he holed out on 61.
Root, playing in his 64th Test, has a 27 percent conversion rate of Test 50s to 100s. Although he put on 138 runs for the third wicket with Cook, his wicket opened the door for the Australians on the placid pitch.
Malan conferred with Cook before deciding not to review, yet replays showed a distinct 'hot spot' nick on his bat which would have kept him at the crease if he had challenged the decision.
It follows James Vince's similar dismissal on Wednesday to Hazlewood for 17, when he also did not seek a review despite 'hot spot' showing a mark on his bat.
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