Root missed the first Test at the Ageas Bowl, Southampton to attend the birth of his child, with Ben Stokes taking the reins in his absence.
Denly, who averages under 30 in Tests, was dismissed for 18 and 29 in England’s four-wicket defeat by West Indies in the opening Test.
Root will slot into his usual number four role, while Zak Crawley, who struck an impressive 76 in the second innings at Southampton, will move up to three.
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“It’s never an easy decision, never easy having to leave someone out,” Root told British media on Wednesday.
“With Joe over a period of time he’s done a brilliant job for us, he’s helped show our identity as a side and how we played moving forward. It’s a very difficult decision but we’ve gone a different way.
“You watch Zak’s progression since he’s been involved in the team, his game has continued to get stronger.”