The big-hitting Jamaica left-handed opener suffered the injury while warming up and was ruled out shortly before the toss, with Kyle Hope taking his place.
A team spokesman later confirmed that Gayle had injured his right hamstring and would be having a hospital scan to assess the extent of the damage.
"Chris Gayle came to me before the toss and said he was feeling something in his hamstring," West Indies captain Jason Holder told BBC Radio's Test Match Special after he sent England into bat.
"He came to me as I was walking up to the coin so I don't know the extent of the injury," the all-rounder added.
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Thursday's fixture was the second of a five-match series that concludes in Southampton a week on Friday.
Gayle only recently arrived in Britain for the limited- overs leg of the tour, having missed West Indies' 2-1 Test series loss to England.
He effectively made himself ineligible for selection by not playing first-class cricket in the Caribbean, having become a well-paid globe-trotting star of the Twenty20 game.
Gayle followed up with a brisk 37 before he holed out in the first ODI at Old Trafford on Tuesday, a match West Indies lost by seven wickets.
That defeat meant the two-time former champions could no longer gain direct entry to the 2019 World Cup in Britain and would have to enter a qualifying competition instead.
Jonny Bairstow, fresh from his 100 not out -- a maiden ODI century -- on Tuesday, was nine not out, with Alex Hales 10 not out on his Nottinghamshire home ground.
Rain was still falling more than two hours later, although plenty of hardy spectators, some sheltering beneath umbrellas, remained in the hope of seeing yet more cricket.
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