I do not claim that this is the earliest example of an epigraph, but as it is earlier than the examples mentioned in the existing answers it is worth posting.
Maimonides wrote دلالة الحائرين (Dalālat al-ḥā’irīn), translated into Hebrew as מורה נבוכים (Moreh Nevuchim) and English as Guide for the Perplexed, at the end of the Twelfth Century. The work begins with a short letter to his student for whom it was written, followed by a preface. The preface begins with an epigraph of three Biblical verses:
"Cause me to know the way wherein I should walk, for I lift up my soul unto Thee." (Psalm cxliii. S.)
"Unto you, O men, I call, and my voice is to the sons of men." (Prov. viii. 4)
"Bow down thine ear and hear the words of the wise, and apply thine heart unto my knowledge." (Prov. xxii. 17.)
My primary object in this work is to explain certain words occurring in the prophetic books. Of these some are homonyms, and of their several meanings the ignorant choose the wrong ones; other terms which are employed in a figurative sense are erroneously taken by such persons in their primary signification. There are also hybrid terms, denoting things which are of the same class from one point of view and of a different class from another. It is not here intended to explain all these expressions to the unlettered or to mere tyros, a previous knowledge of Logic and Natural Philosophy being indispensable, or to those who confine their attention to the study of our holy Law, I mean the study of the canonical law alone; for the true knowledge of the Torah is the special aim of this and similar works.
To preclude the possibility that these verses were added by a more recent copyist/translator, below are several medieval manuscripts in which you can see the epigraph. Note how in every single one the epigraph is visually distinguished from the main text. Thus, even if they had no official term for this, it seems that they were well aware that it wasn't part of the regular text.
The National Library of France, Paris, France Ms. hebr. 685
The British Library, London, England Harley 7586B
The British Library, London, England Add. 14763
The British Library, London, England Harley 7586A
The British Library, London, England Harley 5507
The National Library of France, Paris, France Ms. hebr. 687
The Palatina Library, Parma, Italy Cod. Parm. 3208
Laurentian Library, Florence, Italy Ms. Plut.III.12