Humiliated in an innings and 209-run defeat in the first Test, the tourists hit back to complete a sensational five- wicket victory, inspired by a pair of centuries from Barbados batsman Shai Hope.
Writing in The Times on Wednesday, Atherton said England fans expecting to see another comfortable home win instead witnessed "a resurrection... Of a once-proud cricketing nation fallen on hard times".
"This was one of the great modern Test matches, one that produced a truly astonishing result," he added.
"No one gave West Indies a prayer before the match, nor before the last day."
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It was West Indies' first Test win in England in 17 years and only their fourth Test win away from home against a team other than Bangladesh and Zimbabwe in 20 years.
Hope, 23, had not scored a century in his 11 previous Tests, but became the first man to amass two hundreds in a first-class match at Headingley in the ground's 127-year history.
"These two players, 24 and 23 years of age respectively, represent the future of West Indies cricket and, on this evidence, greener pastures lie ahead," Atherton wrote.
"Brathwaite will become a high-class accumulator, but Hope has the chance to be even better than that, stylish and fluent as he is.
"He has always been known for eye-catching shots but, here, in the course of two innings, he became a Test match batsman in the round, attaching those shots to a cast-iron defence and a commitment to lasting the course."
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