Wealthier countries will be able to access vaccines but will be expected to self-finance, it added.
As well as creating the emergency stockpile, Gavi will also support targeted preventative vaccination outside of an outbreak in high-risk populations, such as health workers, in countries at risk.
The target populations and scope of countries will be based on future recommendations by the World Health Organisation's Strategic Advisory Group of Experts on Immunisation (SAGE).
"Just five years ago we faced an Ebola outbreak in West Africa with no vaccine and no way to treat the disease," Ngozi Okonjo-Iweala, Chair of the Gavi Board, said in a statement.
"Today, thanks to the heroic efforts of countless patients, health workers, scientists, manufacturers, donors, partners as well as the leadership of African countries, we now have one vaccine approved for use and more on their way, as well as rapid diagnostics and several promising treatments," Okonjo-Iweala said.
The WHO's SAGE Working Group on Ebola Vaccines and Vaccination has provided guidance that the global emergency stockpile should be maintained at 500,000 licensed doses of vaccines.