Alyson Lee, 66 and Diane Bligh, were bailed to appear at Westminster magistrates' court on February 11 and 12.
"The women were arrested after a substance, believed to be a powdered paint, was sprayed on an area inside Westminster Abbey," London's Metropolitan police said.
Just Stop Oil (JSO) said two of its supporters spray-painted with chalk "1.5 is dead" on the 19th-century biologist's grave.
Monday's action took place after Europe's climate monitor announced that the last two years saw average global temperatures exceed the critical 1.5C warming limit for the first time.
"Darwin would be turning in his grave to know we are in the midst of the sixth mass extinction," the activists said in a video posted on social media.
The protest took place after fires ravaged Los Angeles in the United States, levelling neighbourhoods, displacing tens of thousands and killing 24.
Formed in 2022, JSO has staged numerous climate-related demonstrations against British and global environmental policies.
Its stunts have drawn condemnation for targeting iconic paintings like Vincent van Gogh's "Sunflowers" with soup and the megalithic standing stones at Stonehenge with orange paint powder.
JSO and its supporters have in turn accused the UK justice system of handing down harsh sentences to its activists.
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