It is thought to be the first time a single strain of an infection has spread so widely in the wake of the virus.
The study, first to identify the separate cases as a single epidemic, found that one in four people in Africa infected with the strain had died.
Cases of this form of invasive non-typhoidal Salmonella have been recognised in Africa for more than a decade. It causes fever, headaches, respiratory problems and sometimes death, the 'BBC News' reported.
Researchers analysed the genetic code of 179 batches of Salmonella from different parts of Africa and the rest of the globe.
Using techniques similar to a large-scale DNA paternity test, they were able to construct the strain's "family tree" and then how it spread.
"It quite clearly parallels the emergence of HIV in Africa, " Prof Gordon Dougan, from the Sanger Institute in Cambridge in the UK, said.
HIV attacks the immune system and leaves people more vulnerable to other infections. It is thought the strain of Salmonella Typhimurium took advantage of this weakness to spread.
Researchers said the bacterium was given the chance to "enter, adapt, circulate and thrive".
There is poor monitoring data for the disease across the whole of the continent, but Dougan said it was affecting "thousands and thousands" of people and that 98 per cent of adult cases were in people with HIV.
The study is published in the journal 'Nature Genetics'.
