The earliest mention I could find is in Alfred Delvau's 1864 edition of his dictionary of French sexual slang, Dictionnaire érotique moderne. His definition (that you can read here) is itself provided in sexual slang, though he gives his readers an explanation of how the 6 and 9 actually work (because it was not obvious). The dictionary, published under a pseudonym (Professeur de langue verte, ie "Teacher of slang") caused him some legal problems. Delvau died in 1867 and his work was later published under his real name. The verses cited as an example by Delvau (it's a dictionary after all!) ("Sixty-nine and his prick gets up again / Sixty-nine could give a hard-on to a dead man") are from an "Anonymous modern song", which is actually the classic porn song Le plaisir des dieux ("Pleasure of the Gods"), published in an anthology of erotic poems (Le Parnasse satyrique du dix-neuvième siècle) at about the same time (mi-1860s). The Plaisir lists several sex acts, and calls the 69 by its name, so we can guess that it was already in use by then. However, the name fails to turn up in older works: for instance, L'art de foutre en quarante manières ("The art of fucking in forty different ways") has a lengthy and precise description of the act but does not really name it other than by the term gamahucher, which usually slang for cunnilingus. So perhaps the "69" term emerged in the first half of the century (gamahucher is older).

In any case, "69" was pretty much established in the latter half of 19th century France. In 1877, Guy de Maupassant himself dedicated an entire poem to it (titled 69) which is not just NSFW but NSFL. This poem, like Le plaisir des Dieux, seems to have been used as a classic song in hospital staff rooms where doctors came to blow off steam (these rooms were until recently decorated with pornographic frescoes).

"69" also pops up in a couple of amusing places: the parodic limination leaves of pornographic books printed anonymously. The pretty women of Paris, a directory of Parisian courtesans written by an anonymous Englishman in 1883, was supposed to have been printed at "69 rue des Déchargeurs", a real street in Paris but "décharger" also means "to ejaculate". Likewise, the Etrennes aux trois sexes of 1889 was printed in "69 copies" by a printer named La Couille d'Or (the Golden Ball).