Chancellor George Osborne and Gates announced 3 billion pounds ($4.28 billion, 4 billion euros) in funding over the next five years for research and to support efforts to eliminate the mosquito-borne disease, in a joint article in The Times.
"When it comes to human tragedy, no creature comes close to the devastation caused by the mosquito," the two wrote.
"We both believe that a malaria-free world has to be one of the highest global health priorities."
The fund would be made up of 500 million pounds a year from Britain's overseas aid budget for the next five years, as well as $200 million this year from The Gates Foundation, with more donations to follow.
There were 438,000 malaria deaths in 2015, most of them of children aged under five, and the majority of them in Africa, according to the World Health Organization.
Efforts to control the disease have made significant progress in the last 15 years, but are threatened by the spread of resistance to antimalarial drugs and to insecticide, the WHO said in its World Malaria Report 2015.
"If new insecticides are not introduced by 2020, the situation will become critical and deaths could surge," Osborne and Gates wrote, adding that fighting diseases required collaboration between private companies, governments and charities.
"We are optimistic that in our lifetimes we can eradicate malaria and other deadly tropical diseases, and confront emerging threats, making the world a safer place for all," the article concluded.
It comes days after the philanthropist Gates announced plans for a $100 million scheme to cut malnutrition in Nigeria.