Anglican priest Sue Parfitt, 82, and retired teacher Judy Bruce, 85, held up a sign saying "The government is breaking the law" after attaching themselves to the display case on Friday, according to Just Stop Oil.
London's Metropolitan police said two women had been charged with criminal damage and released on bail.
The British Library said the damage to the glass case had been "minimal".
"Magna Carta itself remains undamaged," it said, adding that the gallery that houses the display would remain closed until further notice.
Magna Carta is seen as a precursor of democracy and the basis of legal systems across the world as well as human rights conventions.
Dating from June 1215, the Great Charter -- considered one of the world's most important documents -- first put into writing the principle that the king and his government were not above the law.
The two women will appear before magistrates in London on June 20.
Just Stop Oil wants the UK government to end all new oil and gas exploration and has promised not to let up in its protests until it does so.
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