Stokes spent 39 balls to score 12 runs for Durham.
Kasey Alridge, Durham captain, won the toss and chose to bat first, but found the going tough. Batters struggled for runs, with Will Rhodes (31) and Colin Ackerman (26) being the only ones to cross the 20-run mark as Durham folded for 165 runs in 48.1 overs.
Kuldeep Yadav finished with 2/23 in his 10 overs, and one of his wickets was Ben Stokes, the former England captain.
The England all-rounder tried a reverse sweep to get free after spending 39 deliveries at the crease for just 12 runs. But all he could do was direct the ball to backward point, where George Hill made a simple catch.
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Kuldeep’s second wicket came in the form of Colin Ackermann, who looked set after scoring 26 before becoming another victim of the Indian spinner.
Yorkshire lost Adam Lyth and William Luxton early, but Will Bennison (36), James Wharton (56*) and Sam Whiteman (48*) kept the team on track for the win.