There are a few different meanings of the two, which are worth considering separately.
He paid £5 over and above the agreed minimum repayment.
Such uses state an amount to which something is over what is required.
He gave service over and above the call of duty.
Such use has an implication of particularly strong action. A soldier who does an extra hour's work on a detail would not be spoken of as having acted "over and above", though he or she literally speaking did, because the phrase is associated with particularly notable acts of self-sacrifice.
The law of God is over and above the law of Man.
Such a statement claims plainly that the rule of God over-rules the rule temporal government, but the emphasis implied by the use of both over and above suggests that it is not just greater, but so much greater as to be of a different order.
Note that in the last two cases are as much a matter of nuance than of strict meaning. Stricly anything that is greater or beyond another thing can be called "over and above", but the phrase implies that it is much greater, except in those cases where we can quantify the difference (as in the first case).