If you want (or need) to do it as a Riemann sum, your best bet is to change the index of summation, letting $k=n^2-i$, which runs (backwards) from $0$ to $n^2-1$ as $i$ runs from $1$ to $n^2$. Since $i=n^2-k$, we have $i/n-n=(n^2-k)/n-n=-k/n$, so that we get
$$\lim_{n\to\infty}{1\over n}\sum_{k=0}^{n^2-1}e^{-k/n}=\int_0^\infty e^{-x}dx$$
If you really need the result in the form given, you can let $k=i-n^2$ instead, so that $k$ runs from $1-n^2$ to $0$, and write
$$\lim_{n\to\infty}{1\over n}\sum_{k=1-n^2}^0e^{k/n}=\int_{-\infty}^0 e^xdx$$
(Ah, I just now noticed Clement C's comment below the OP, which says exactly the same thing.)
Added later, in response to the OP's question in comments: This is not a standard Riemann sum, in which the interval is fixed and it's just the partition that's getting finer and finer. In this case, $\Delta x={1\over n}$ as usual, but, because $k$ runs from $0$ to $n^2-1$ (in the first displayed equation -- the second one is analogous), $x=k/n$ takes values from $0$ to $n-{1\over n}\approx n$. The upshot is that, for any given (large) $n$, we should (and do) have
$${1\over n}\sum_{k=0}^{n^2-1}e^{-k/n}\approx\int_0^ne^{-x}dx$$
Because it's a somewhat nonstandard Riemann sum, some extra care is technically called for in proving that it converges to the (improper) integral $\int_0^\infty e^{-x}dx$. This is what zhw. does in his/her answer.