Answer

First, Esau was an apostate Jew, and it is not clear to me when he apostatized. It is possible that he was still Jewish.
Beyond that, a single witness in matters of prohibition is not testimony but evidence, so there are no formal rules here: when there is evidence, it is admissible. This is a factual question, not a halakhic one.
And third, this was before the giving of the Torah, so it is doubtful to what extent they followed the laws of testimony there, and certainly the laws of testimony of Jewish law. Admittedly, that is not necessarily an argument, because the whole matter is midrashic/aggadic literature and not a factual description, so one can prove that a gentile single witness is trusted from the fact that the Sages constructed the midrash this way, even if it did not really happen and even if before the giving of the Torah all this is irrelevant. But then that is evidence that this is what the Sages held, not a source showing from where they learned it. But from the first two points I made above, you can also understand from where they learned it.