They can't know that for certain! See Lee Berger's announcement video [1] for a discussion. Paraphrasing the slide:

    There is no evidence of *homo sapiens* use or presence beyond the light zone of the cavern system
    Cultural context: there are *homo nadeli* graves in the cave system with the drawings
    Access to the cavern system has not changed and would have been much easier for the smaller *homo nadeli* (Lee Berger had to lose 55 pounds to fit into the caves)
    The burials and drawings were made over a long period of time, implying an ongoing settlement
    The evidence for *homo nadeli* burials meets or exceeds that accepted for ancient *homo sapiens* burials

That last bit is the most interesting one. Since there are almost no fluvial or geological changes in the cavern system over hundreds of thousands of years, the graves of the homo nadeli are much better preserved than ancient homo sapien graves. By comparing the layers of dirt in the grave and the rest of the cave system, they can determine to a high degree of certainty that it was in fact a purposeful burial instead of a random "body in a hole".

[1] https://youtu.be/fFbgQhY4Yxw?t=1058