There are multiple questions implicit in this question.
How do you define an equivalent of the controlled-not for qutrits?
There are probably multiple ways that the gate can be generalised, but this paper defines it as
$$
|x\rangle|y\rangle\mapsto|x\rangle|-x-y\text{ mod }3\rangle
$$
I'm not sure why they use the - sign, and am instead going to take the definition
$$
|x\rangle|y\rangle\mapsto|x\rangle|x+y\text{ mod }3\rangle
$$
That means that we can write the unitary matrix as
$$
\left(\begin{array}{ccccccccc}
1 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 0 \\
0 & 1 & 0 & 0 & 0 & 0 & 0 & 0 & 0 \\
0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 0 \\
0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 \\
0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 \\
0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 \\
0 & 0 & 0 & 0 & 0 & 0 & 0 & 0 & 1 \\
0 & 0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 \\
0 & 0 & 0 & 0 & 0 & 0 & 0 & 1 & 0
\end{array}\right).
$$
Is it possible to realise this gate in 3 dimensions?
Sure, why not? This paper talks defines things slightly differently, but one could construct the gate I've specified using their formalism, and they also discuss some ideas for physical implementation. This paper may also be interesting.
Has this gate been realised?
Not to my knowledge, but I can't pretend to know everything that has every been achieved experimentally. I would point out, however, that this paper is only doing single-qudit gates, not two-qudit gates. Judging by the fact that that paper was only last year, I'd guess the two qudit generalisation hasn't been done yet in that particular physical realisation.