The money raised from the partnership will be used to fund a new service for people affected by breast or prostate cancer.
As the official charities in 2012, Breast Cancer Care and the Prostate Cancer Charity will get 250 gold bond places and an increased brand profile on the marathon site.
A spokeswoman for the Prostate Cancer Charity said the charities were hoping to raise £1m from the marathon between them.
A spokesman for Virgin Money confirmed it was the first time that two charities had shared the position.
"We liked the proposal because it was creative – it included men and women and they will be using the money to fund sport," he said. "All of those factors together made it seem like a proposal we wanted to take forward."
The children's cancer charity Clic Sargent, which was the official charity for 2010, raised more than £2m with 700 runners participating on its behalf.
The official charity for this year's marathon, which takes place on Sunday, is Oxfam. A spokesman for the charity said it had about 500 runners taking part and it hoped to raise £1m.