The Metropolitan Police said the pair were arrested for "suspicion of causing criminal damage" and taken to a central London police station for questioning.
They had scaled the Gothic tower with ropes at dawn, and once at the west clock face they unfurled a small banner with the words "Time for the truth" in sight of live television cameras below.
But high winds foiled their plans to stay on Big Ben all day, and early in the afternoon they slid back down to the ground, at around the same time that an anti-war march set off from Hyde Park for Trafalgar Square.
Stephen Tindale, executive director of Greenpeace, told reporters: "It's time we got the truth about why thousands of people had to die in a war that the world did not want."
Police said they were reviewing security at the Houses of Parliament, of which Big Ben is the best-known section, but added that at no time were the two protesters in a position to break into the premises.
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