Kemar Roach took 2-28, including clean bowling Stokes, and an instinctive slip catch accounted for the wicket of Rory Burns, who scored 57.
Ollie Pope (24 not out) and Jos Buttler, who has two runs to his name, were unbeaten after the second session on Friday as the West Indies were looking to get among the lower order after England sacrificed a batsman in their line up to include an extra seamer after injury to Stokes.
England's talisman looked uncomfortable at the crease as he struggled with a quadriceps strain, picked up during his second test heroics, and made only 20 runs.
He was cleverly set up by Roach, who after two bouncers produced a perfect in-swinging delivery to strike down the stumps as England slumped to 92-3.
Skipper Root was the second wicket to fall after being caught short as England attempted a quick single and dismissed for 17 runs.
Joe Root of England plays a shot during Day One of the Ruth Strauss Foundation Test, the Third Test in the #RaiseTheBat Series match between England and the West Indies at Emirates Old Trafford on July 24, 2020 in Manchester, England.
Image credit: Getty Images
Burns and Root had put on 46 runs for the second wicket before Burns set off for a quick run after steering spinner Rakheem Cornwall towards third man. Roston Chase fielded quickly and hit the stumps with direct throw, catching the scrambling Root short of the crease, to the delight of the fielding team.
Burns proved the steady presence after England were put into bat by the tourists and lost Dom Sibley to just the sixth ball of the day, trapped leg before wicket without scoring.
Burns brought up his half century in 126 balls with just three boundaries but then cut a spinning delivery from Chase to Cornwall at first slip, who took a reflex one-handed catch to an aghast reaction from his team mates.
Pope and Buttler are the last recognised batsmen for England. Buttler's place in the team was the subject of much speculation in recent weeks after poor returns with the bat.
West Indies won the first test in Southampton by four wickets but England took the second at Old Trafford by 113 runs.