The X-ray source populations within galaxies are typically difficult to identify and classify from X-ray data alone. We are able to break through this barrier by combining deep new Chandra ACIS-I observations with extensive Hubble Space Telescope imaging from the PHAT survey of the M31 disk. We detect 373 X-ray sources down to 0.35-8.0 keV flux of 10$^{-15}$ erg cm$^{-2}$ s$^{-1}$ over 0.4 square degrees, 170 of which are reported for the first time. We identify optical counterpart candidates for 188 of the 373 sources, after using the HST data to correct the absolute astrometry of our Chandra imaging to 0.1$$. While 58 of these 188 are associated with point sources potentially in M31, over half (107) of the counterpart candidates are extended background galaxies, 5 are star clusters, 12 are foreground stars, and 6 are supernova remnants. Sources with no clear counterpart candidate are most likely to be undetected background galaxies and low-mass X-ray binaries in M31. The 58 point sources that are not consistent with foreground stars are bright enough that they could be high mass stars in M31; however, all but 8 have optical colors inconsistent with single stars, suggesting that many could be background galaxies or binary counterparts. For point-like counterparts, we examine the star formation history of the surrounding stellar populations to look for a young component that could be associated with a high mass X-ray binary. For the 40 point-like counterpart candidates associated with young populations, we find that their age distribution has two peaks at 15-20 Myr and 40-50 Myr. If we only consider the 8 counterpart candidates with typical high-mass main sequence optical star colors, their age distribution peaks mimic those of the sample of 40. Finally, we find that intrinsic faintness, and not extinction, is the main limitation for finding further counterpart candidates.
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