Hundreds of thousands of people die from malaria every year and it is the parasite Plasmodium falciparum, the type researchers studied, that accounts for most cases.
African great apes were the original host to the parasite, they said, intoning that a chance genetic mutation about 50,000 years ago turned it into a threat to humans.
Researchers at the Wellcome Sanger Institute hope that the findings, published in the journal PLoS Biology, could help uncover new ways to fight malaria.
Malaria is caused by a parasite that gets into the bloodstream when an infected mosquito bites humans - or animals.
There are lots of different strains of parasite and one of the most important ones, which now affects only humans, is Plasmodium falciparum.
It switched host from gorillas at a time that there was a big migration of humans out of Africa, estimated at some 40,000 to 60,000 years ago.
They studied the genetic make-up of different ancestral types of the malaria parasite, focusing in particular on a gene called rh5 - the vital bit of DNA code that enables malaria to infect human red blood cells.
It is a target doctors are very interested in for developing workable malaria vaccines, including improving on a malaria vaccine rolled out for tens of thousands of children.
The researchers assert that tens of thousands of years ago, two types of malaria parasite happened to co-infect a gorilla and they exchanged some genetic material between them.
It was at that point that Plasmodium falciparum picked up the rh5 gene, they argued.
Lead author Dr Gavin Wright said this was a rare event that led to so much death and disease in humans.
"We were quite surprised by the findings. It was very satisfying because it makes sense with lots of other research that has been done by colleagues. It provides this molecular explanation now as to how this jump could have occurred.
"Rh5 currently is an important blood stage vaccine candidate for malaria and so if we can get any more information on this gene, that could really help us in trying to combat this disease."
He said the chances of the parasite mutating again soon were slim to the extreme, although theoretically possible. Nearly half of the world's population is exposed to the risk of malaria, with the most cases and deaths occurring among young children in sub-Saharan Africa, the work of Plasmodium falciparum.