Their study, published in Nature Genetics, is the first to identify the separate cases as a single epidemic.
One in four people in Africa infected with the strain died.
It is thought to be the first time a single strain of an infection has spread so widely in the wake of HIV.
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 research team 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 happened in two waves. The first started in south-eastern Africa about 52 years ago and the second wave started 35 years ago from the Congo Basin.
Prof Gordon Dougan, from the Sanger Institute in Cambridge in the UK, told the BBC: "It quite clearly parallels the emergence of HIV in Africa."
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 and spread. The research team 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 Prof Dougan said it was affecting "thousands and thousands" of people and that 98% of adult cases were in people with HIV.
He said this spread of Salmonella Typhimurium had been different to that of other infections commonly associated with HIV, as it had been a single epidemic "people were completely unaware" of and there "were not really any other examples" of that happening.
Dr Melita Gordon, a gastro-enterologist at the University of Liverpool, said: "It's the first time this has been described right across a continent in such an obvious way."
She added: "The highest mortality associated with the disease is 80%. What's happened over the years is mortality has fallen down and down and down to between 20% and 25% as doctors inside Africa recognise it."
The genetic analysis also showed the strain was resistant to the first choice antibiotic, chloramphenicol, which means more expensive drugs would be needed to treat the infection.
It is thought that improving HIV treatment across Africa could reduce the prevalence of the Salmonella infection, as it would reduce the number of people with vulnerable immune systems. However, the researchers urged "vigilance" in case the Salmonella strain mutated again to become able to infect people with healthy immune systems.
Commenting on the study, Prof Brendan Wren, from the London School of Hygiene and Tropical Medicine, told the BBC: "It's actually quite a huge problem and it seems to be getting worse because there are many susceptible people, it's got a grip in Africa.
"HIV, I think it's fair to say, provided a springboard for it to take off."
However, he thought the disease was "near its peak" as HIV was more controlled in other continents giving it little room to spread.
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