I'm not sure about this specific case, but they can use uranium-lead dating, looking at its isotopes, to determine stones several million years old. They examine the rock the fossil is in to determine the fossil's age. They also combine that technique with some confirmation techniques: examining the bones of the other animals found with the homonids, knowing the time period those animals were alive; looking at the plants in the same stone layers and knowing those time periods; they also look at the stone tools (or lack thereof) knowing how tools evolved to help confirm the age.

* https://en.wikipedia.org/wiki/Uranium%E2%80%93lead_dating

> A fossil hominin cranium was discovered in mid-Pliocene deltaic strata in the Godaya Valley of the northwestern Woranso-Mille study area in Ethiopia. Here we show that analyses of chemically correlated volcanic layers and the palaeomagnetic stratigraphy, combined with Bayesian modelling of dated tuffs, yield an age range of 3.804 ± 0.013 to 3.777 ± 0.014 million years old (mean ± 1σ) for the deltaic strata and the fossils that they contain.

https://www.nature.com/articles/s41586-019-1514-7