Yes, scientists have recently confirmed that the Justinianic plague of 543 AD was indeed caused by Y. Pestis, the microbe which causes bubonic and pneumatic plague.
See: David M Wagner et al., “Yersinia Pestis and the Plague of Justinian 541–543 AD: A Genomic Analysis,” The Lancet Infectious Diseases 14, no. 4 (April 2014): 319–26, doi:10.1016/S1473-3099(13)70323-2.
Has science been able to discover the bug that was behind the plague of Pericles?