TL;DR: three relatively easy bounds are the numbered equations below.
You cannot directly apply the formula for the geometric series for the reason mentioned in your edit. But note that $i\geq1$, so we have $$\sum_{i=1}^n{\exp{\left(-\frac{i^2}{\sigma^2}\right)}}\leq\sum_{i=1}^n{\exp{\left(-\frac{i\cdot1}{\sigma^2}\right)}}$$ The latter, of course, is a geometric sum. Taking the sum over all $i$ (including $i=0$), we get $$(1-e^{-\sigma^{-2}})^{-1} \tag{1} \label{eqn:first}$$ The calculation for finitely many terms isn't much harder, and only differs by an exponentially decreasing factor.
If this isn't a strong enough bound, there are other techniques. If $n<\sigma$, then we can get very far elementarily. Note that $e^x\geq x+1$; dividing each side, we get $$e^{-x}\leq(1+x)^{-1}=\sum_{k=0}^{\infty}{(-x)^k}$$ if $|x|<1$. Taking $x=\left(\frac{i}{\sigma}\right)^2$, we thus obtain \begin{align*}
\sum_{i=1}^n{e^{-\frac{i^2}{\sigma^2}}}&\leq\sum_{i=1}^n{\sum_{k=0}^{\infty}{\left(-\left(\frac{i}{\sigma}\right)^2\right)^k}} \\
&=\sum_{k=0}^{\infty}{(-1)^k\sum_{i=1}^n{\left(\frac{i}{\sigma}\right)^{2k}}} \tag{*} \label{eqn:star}
\end{align*}
(We can interchange sums because one is finite.) Now, for all $k$, the function $\left(\frac{\cdot}{\sigma}\right)^{2k}$ is increasing on $[0,\infty)$; we thus have $$\int_0^n{\left(\frac{i}{\sigma}\right)^{2k}\,di}\leq\sum_{i=1}^n{\left(\frac{i}{\sigma}\right)^{2k}}\leq\left(\frac{n}{\sigma}\right)^{2k}+\int_1^n{\left(\frac{i}{\sigma}\right)^{2k}\,di}$$ Evaluating the integrals and simplifying, we have $$0\leq\sum_{i=1}^n{\left(\frac{i}{\sigma}\right)^{2k}}-\frac{n}{2k+1}\left(\frac{n}{\sigma}\right)^{2k}\leq\left(\frac{n}{\sigma}\right)^{2k}\left(1-\frac{1}{(2k+1)n^{2k}}\right)$$
Substituting into $\eqref{eqn:star}$, we get \begin{align*}
\sum_{i=1}^n{e^{-\frac{i^2}{\sigma^2}}}&\leq\sum_{k=0}^{\infty}{\frac{(-1)^kn}{2k+1}\left(\frac{n}{\sigma}\right)^{2k}}-\sum_{j=0}^{\infty}{\left(\frac{n}{\sigma}\right)^{4j+2}\left(1-\frac{1}{(4j+3)n^{4j+2}}\right)} \\
&\leq\sum_{k=0}^{\infty}{\frac{(-1)^kn}{2k+1}\left(\frac{n}{\sigma}\right)^{2k}}-\sum_{j=0}^{\infty}{\left(\frac{n}{\sigma}\right)^{4j+2}} \\
&=\sigma\tan^{-1}{\left(\frac{n}{\sigma}\right)}-\frac{\left(\frac{n}{\sigma}\right)^2}{1-\left(\frac{n}{\sigma}\right)^4}\hspace{4em}(n<\sigma) \tag{2}
\end{align*}
Finally, for the general case we can achieve a slight improvement on $\eqref{eqn:first}$ via the theory of majorization. $\{x_i\}_{i=1}^n\mapsto\sum_{i=1}^n{\exp{\left(-\frac{x_i}{\sigma^2}\right)}}$ is convex and symmetric in its arguments, hence Schur-convex. Let $b_i=i^2$ and $a_i=\left(\frac{2n-1}{3}\right)i$. Clearly, for all $m\leq n$, we have $$\sum_{i=1}^m{a_i}=\frac{m(m-1)}{2}\cdot\frac{2n-1}{3}\geq\frac{m(m-1)(2m-1)}{6}=\sum_{i=1}^m{b_i}$$ with equality if $m=n$. Thus $\vec{a}$ majorizes $\vec{b}$, so \begin{align*}
\sum_{i=1}^n{\exp{\left(-\frac{i^2}{\sigma^2}\right)}}&=\sum_{i=1}^n{\exp{\left(-\frac{b_i}{\sigma^2}\right)}} \\
&\leq\sum_{i=1}^n{\exp{\left(-\frac{a_i}{\sigma^2}\right)}} \\
&=\sum_{i=1}^n{\exp{\left(-\frac{(2n-1)i}{3\sigma^2}\right)}} \\
&\leq\sum_{i=0}^{\infty}{\exp{\left(-\frac{(2n-1)i}{3\sigma^2}\right)}} \\
&\leq\left(1-\exp{\left(\frac{2n-1}{3\sigma^2}\right)}\right)^{-1} \tag{3}
\end{align*}