Separation of church and state is both the first amendment and a clause in article six of the constitution:

First Amendment:

Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof

article six

no religious Test shall ever be required as a Qualification to any Office or public Trust under the United States.

Thomas Jefferson's use of the words "separation of church and state" was to explain the purpose of the first amendment specifically but the actual legal text of the constitution is worded broadly enough to cover not only separation of church and state but separation of mosque/synagogue/ect and state rather than singling out Christianity.