Bairstow and Stokes looked bemused but Australia refused to withdraw the appeal and the right-hander trudged off to loud boos around the ground.
Stokes, clearly fired up to play another match-winning innings as he did in the 2019 Ashes, went on the attack.
Duckett and Stokes had batted cautiously after England resumed on 121-4, milking singles from the predominantly short-pitched bowling they faced.
Stokes, on 39, was given out lbw to Mitchell Starc but the batsman reviewed immediately and replays showed the ball had hit the bat before striking his pad.
Reporting by Ed Osmond; Editing by Hugh LawsonOur Standards: The Thomson Reuters Trust Principles.
Persons:
Ben Stokes, Australia's Cameron, Peter Cziborra LONDON, Jonny Bairstow, Stokes, Bairstow, Alex Carey, Cameron Green, Ben Duckett, Pat Cummins, Green, Duckett, Mitchell Starc, Nathan Lyon, Cummins, Josh Hazlewood, Carey, Stuart Broad, Ed Osmond, Hugh Lawson
Organizations:
England, Australia, Green, Headingley, Thomson
Locations:
Australia, London, Britain, England, Lord's