If Wikipedia is accurate, there isn’t a direct connection between the name that Europeans use to describe the nation, and the name of the saint.
I’ll chime in with Cordoba Spain and its namesake Cordoba Argentina. The Spanish city is much older and more historically significant, having been the a major city of the Moorish culture of Andalusia, but the Argentine city is currently more populous. So I think it comes out about equal.
My city of Syracuse, NY is named after Sicily, Italy. From Wiki:
The name Syracuse was chosen, after Syracuse , Sicily, because of similarities such as a salt industry and a neighboring village named Salina. Syracuse, NY was originally a town but later grew into a city.
Not exactly what the OP was asking for, but Jim Gaffigan has a funny bit in his latest show from Canada about St. John, New Brunswick, and St. John’s, Newfoundland.
In a way, San Juan, Puerto Rico, fits in here too - the same name in a different language.