As the players guarded the pitch, one was picked up by Bairstow and another stopped by England captain Ben Stokes.
The powder did land on the square, but was cleared by groundstaff and the game resumed after a short delay.
■ Follow live updates from the second Test between England and Australia
The Metropolitan Police said three arrests were made after the protest.
Guy Lavender, chief executive of Marylebone Cricket Club (MCC) which owns Lord's, said he condemned the protest "in the strongest possible terms".
"Their actions not only endanger themselves and those who work at the ground, but they have consistently shown complete disregard for the people who pay to attend events, not just here at Lord's but around the country at other sporting venues," he said. A Just Stop Oil spokesperson said: "Cricket is an important part of our national heritage, but how can we enjoy the Ashes when much of the cricketing world is becoming unfit for humans to live in?
"We can no longer afford to distract ourselves when the sports we play, the food we eat, and the culture we cherish is at risk.
"It's time for cricket lovers and all those who understand the severity of this situation to get onto the streets and demand action."
Just Stop Oil protesters have disrupted other sporting events this year, including the rugby union Premiership final and the World Snooker Championship.
The environmental protest group is calling for the government to halt all new oil, gas and coal projects.
■ Just Stop Oil: What is it and what does it want?
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