Five-time Indian Premier League winner Fleming will replace compatriot Brendon McCullum, who lost his role in charge of the Test set-up after a 2-1 home series loss to New Zealand in June, which followed a disastrous Ashes campaign.
Ben Stokes stepped down as Test captain and retired from international cricket after defeat at Trent Bridge last month and the England and Wales Cricket Board announced on Thursday that Root will step up to fill the void.
The decision to return to Root, who has captained England in 65 Tests, will allow all-format player Harry Brook to focus on the white-ball captaincy ahead of next year's World Cup.
Root will resume his reign as captain in the three-match series with Pakistan in August, but ex-Chennai Super Kings coach Fleming will not be in charge.
Marcus Trescothick will instead act as interim head coach with Fleming back in his homeland to spend time with his family.
"I'm incredibly excited to be joining England as Test coach. It's one of the most prestigious coaching positions in world cricket and I am honoured to be appointed," Fleming said.
"I am looking forward to working with the players and bedding in the gains made by Brendon McCullum and Ben Stokes.
"Of course, the ambition is always to win now. But equally, it's about ensuring the team is well placed for the medium and long-term future.
"There is a lot of young talent in and around the team and our aim is to help them fulfil their potential as world-class cricketers."
Fleming's appointment came after former England chief Andy Flower ruled himself out and after former Australia coach Justin Langer this week revealed he had not been contacted by the ECB.
The 53-year-old appears to hold a close relationship with England white-ball head coach McCullum after they played together on the international scene across a six-year spell.
The Kiwi duo also co-founded digital platform CricHQ in 2015 and were coaching rivals for a period in the Indian Premier League, with Fleming's Chennai Super Kings defeating McCullum's Kolkata Riders in the final of the 2021 edition.
That is one of five IPL triumphs for Fleming, who left his role in charge of Super Kings earlier this summer and has previously coached Southern Brave in The Hundred.
Fleming's departure from Super Kings made him one of the few candidates for the Test job not in an IPL position.
He takes over an England team down in fifth spot in the world Test rankings, without a series triumph in 14 months and on a run of eight defeats across a 13-match spell.
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