The 18th Amendment did not clarify how prohibition was to be enforced. That was done by separate legislation, the Volstead Act. It expressly allows ritual use (including by Jewish communities.) There were also allowances for medicinal uses. Had they not made exceptions for religious use, it would have been a violation of the first amendment protection of free exercise of religion. There is a more recent example - the use of Peyote in Native American rituals, when laws against use were challenged under the 1st amendment. Those rights were partially protected in 1978 by the American Indian Religious Freedom Act, limited to particular groups, and extended in 1994 to others. (AIRFA also allows other religious exceptions, such as use of feathers from protected species, access to some sacred sites and rituals like the Sundance, which had been outlawed... but there is still question on what practices, exactly, are protected.)

Here is the relevant section of the Volstead Act: "Nothing in this title shall be held to apply to the manufacture, sale, transportation, importation , possession, or distribution of wine for sacramental purposes, or like religious rites, except section 6 (save as the same requires a permit to purchase) and section 10 hereof, and the provisions of this Act prescribing penalties for the violation of either of said sections. No person to whom a permit may be issued to manufacture, transport, import, or sell wines for sacramental purposes or like religious rites shall sell, barter, exchange, or furnish any such to any person not a rabbi, minister of the gospel, priest, or an officer duly authorized for the purpose by any church or congregation, nor to any such except upon an application duly subscribed by him, which application, authenticated as regulations may prescribe, shall be filed and preserved by the seller. The head of any conference or diocese or other ecclesiastical jurisdiction may designate any rabbi, minister, or priest to supervise the manufacture of wine to be used for the purposes and rites in this section mentioned, and the person so designated may, in the discretion of the commissioner, be granted a permit to supervise such manufacture."

Source of text: http://www.historycentral.com/documents/Volstead.html

Edited to add AIRFA info.