A vowel was a specific sound made in verbal communication, as opposed to a consonant.
The preservers obelisk on Amerind could be opened either by playing certain musical notes or by speaking a series of vowels and consonants in their proper sequence. (TOS: "The Paradise Syndrome")
A reversal of vowel and consonant was called metathesis, which accidentally made Captain Picard say "Mister Broccoli" instead of Barclay in 2366. (TNG: "Hollow Pursuits")
In a holographic recreation of 1944 France, a message to the French Resistance in Sainte Claire was encrypted in a weather report of the British Radio Network. The code key to decipher it was every fifth letter, every third vowel. (VOY: "The Killing Game")