Protesters have unfurled a large banner reading "throw the money changers out of the temple" on the cathedral steps. The action came as the group marks the anniversary of its now-dismantled protest camp outside the cathedral.
The Dean said he and a member of Occupy Faith, the group's religious wing, were leading a prayer when the women came up and started shouting.
"It will be a long cold night if they want to stay there," he said. "I don't know what they want to do. I'm just sorry they have decided to do this, which makes it hard for members of Occupy Faith, who have been working together with us on something which is respectful."
Occupy London released a statement which said they were collaborating with Christianity Uncut to call for the leadership of St Paul's to "stop sitting on the fence and join the fight against rising inequality in the UK and beyond."
Last year hundreds of people set up camp outside St Paul's on October 15 after they were prevented from entering nearby Paternoster Square, where the London Stock Exchange is located, and remained there for four months. The church, caught in a conflict between the demonstrators and London's finance industry, changed its stance on the camp several times.