late 14c., excepcioun, "act or fact of leaving out or the excluding of" from the scope of some rule or condition, from Anglo-French excepcioun (late 13c. in a legal sense, "formal objection or protest entered by a defendant"), Old French excepcion, from Latin exceptionem (nominative exceptio) "an exception, restriction, limitation; an objection," noun of action from past-participle stem of excipere "to take out" (see except).
From c. 1400 as "a reservation or exemption;" from late 15c. as "something that is excepted." The exception that proves the rule is from law: exceptio probat regulam in casibus non exceptis, "the exception proves the rule in cases not excepted;" exception here being "action of excepting" someone or something from the rule in question, not the person or thing that is excepted. The figure of speech in to take exception "find fault with, disapprove" is from excipere being used in Roman law as a modern attorney would say objection.