A very efficient way to shuffle an array of numbers where each index is unique comes from image processing and is used when applying techniques like pixel-dissolve.
Basically you start with an ordered 2D array and then shift columns and rows. Those permutations are by the way easy to implement, you can even have one exact method that will yield the resulting value at x,y after n permutations.
The basic technique, described on a 3x3 grid:
1) Start with an ordered list, each number may exist only once
0 1 2
3 4 5
6 7 8
2) Pick a row/column you want to shuffle, advance it one step. In this case, i am shifting the second row one to the right.
0 1 2
5 3 4
6 7 8
3) Pick a row/column you want to shuffle... I suffle the second column one down.
0 7 2
5 1 4
6 3 8
4) Pick ... For instance, first row, one to the left.
2 0 7
5 1 4
6 3 8
You can repeat those steps as often as you want. You can always do this kind of transformation also on a 1D array. So your result would be now [2, 0, 7, 5, 1, 4, 6, 3, 8].