In order to make this possible you need to make sure to include the .bbl file in the repository, i.e., keep track of the revisions of that file. Note that this deviates from normal procedure; as the .bbl file is derived one would normally not revise it separately. If you have done this then
latexdiff-vc --flatten -r rev1 -r rev2 file.tex --pdf
should show changes to the bibliography, too (although some bibliography styles do not play well with latexdiff, see the .bbl file generated by latexdiff causes errors for further hints
).
Otherwise, it will get more complicated, and you are probably best off retrieving the two revisions and bbl files for the two revisions manually. Note that you can generally (depending on bibliography style) run latexdiff separately on the bbl files.