Stokes, who was on 10, was not looking at the ball when he blocked it, and his movements appeared to be more self-preservation than any intention of protecting his stumps.
Wicketkeeper Matthew Wade immediately appealed, along with Starc, and umpire Kumar Dharmasena referred the decision to the third umpire Joel Wilson, who gave Stokes his marching orders.
The dismissal reduced England to 4-141, and triggered a collapse of 5-46 before a 55-run partnership between Eoin Morgan (85 off 87) and Liam Plunkett (24 off 12) pushed Australia to the end.
The incident enraged the Lord's crowd, who booed for half an hour and hurled abuse at Starc.
The bowler responded by clean bowling Plunkett to end England's resistance and silence the crowd.
Glenn Maxwell finished with two wickets while Pat Cummins claimed 4-56. Earlier, Mitch Marsh blasted a blistering half century to carry Australia past 300 after Steve Smith (70) and George Bailey (54) had set the platform.
- AAP