「ゆう」 is neither the kun'yomi nor on'yomi of 「昨」 and 「べ」 is not a pronunciation of 「夜」 either. The same can be said about the pronunciation 「きょう」 for 「今日」.
So how come the pronunciations of the two words are like those? If they are special, what was the origin of such pronunciations?
To respond to Mark Hosang answer on ゆうべ, from my dictionary software:
p/s: yup, the "sakuya" pronunciation is also there :)