While international conventions already ban rhino poaching, the number of rhinos killed in South Africa in 2012 was nearly double that of 2010, the BBC reported Monday.
The price of rhino horn used in traditional medicine in Asian countries, especially Vietnam, has soared to $29,500 a pound, higher than gold.
Buyers in Vietnam are paying such prices for rhino horn they believe can cure a number of ills including cancer, officials said.
"The continued slaughter is a cause for immense concern," South Africa's environmental minister, Edna Molewa, said at the signing of the new agreement in the Vietnamese capital Hanoi.
The pact will focus on seven areas of cooperation, with each country to appoint a coordinator to help implement the five-year agreement.
It is the first official agreement on poaching signed by both countries and has been hailed by conservationists.
"Its implementation will of course be down to political will, but the chances are much better if the orders come from high enough in the government," Richard Thomas, a spokesman for the World Wildlife Fund, said.