Hi Fabien,
this is not built-in, but might do something similar to what you require.
f[g[Subscript[x, 1, 1], Subscript[x, 1, 2], Subscript[x, 1, 3]], g[Subscript[x, 2, 1], Subscript[x, 2, 2], Subscript[x, 2, 3]], g[Subscript[x, 3, 1], Subscript[x, 3, 2], Subscript[x, 3, 3]]] /. {g -> f, f -> g, Subscript[c_, a_, b_] -> Subscript[c, b, a]}

It can be done if the indices are part of the variable names like in your case, but it is less elegant. By the way, I usually refrain from using subscripts.
Best wishes,
Marco