This a potential answer to the question. It is not clear whether its proof technique can be completed or not.
We can obtain the result by considering convergence of the Fourier transform of the partial sums. Since $f$ is smooth and compactly supported it is in $L^2(\mathbb{R})$ as are all of its derivatives.
Let $f_n$ be the $n$th partial sum in the series: $f_n = \sum_{j=0}^n \frac{(\partial_x^2)^j}{j!} f$. We can compute the Fourier transform of $f_n$ as:
$$\mathcal{F}(f_n)(k) = \mathcal{F}\left(\sum_{j=0}^n \frac{(\partial_x^2)^j}{j!} f\right)(k) = \sum_{j=0}^n \frac{(2\pi i k)^{2j}}{j!} \hat{f}(k) = \hat{f}(k) \sum_{j=0}^n \frac{(-4\pi^2 k^2)^j}{j!}$$
Therefore (quesionably, see below) $\hat{f}_n \to \hat{f}e^{-4\pi^2 k^2}$ in $L^2(\mathbb{R})$. Then by Plancherel's theorem, $f_n \to \mathcal{F}^{-1}(\hat{f}e^{-4\pi^2 k^2})$ in $L^2(\mathbb{R})$.
Update:
$\hat{f}_n \to \hat{f}e^{-4\pi^2 k^2}$ in $L^2(\mathbb{R})$
There seems to be some disagreement over whether this statement is true so I'll add details (and am unable to complete the proof). As demonstrated above,
$$\hat{f}_n(k) = \hat{f}(k) \sum_{j=0}^n \frac{(-4\pi^2 k^2)^j}{j!}$$
Observe that $\hat{f}$ is in $L^2(\mathbb{R})$ by Plancharel's theorem. Likewise, $\hat{f}(k)e^{-4\pi^2 k^2}$ is in $L^2(\mathbb{R})$ (because $e^x \leq 1$ for all $x \leq 0$).
We want to show that
$$||\hat{f}(k)e^{-4\pi^2 k^2} - \hat{f}_n(k)||_2 \to 0$$
i.e. for all $\epsilon > 0$, there exists an $N$ such that for all $n\geq N$
$$||\hat{f}(k) \sum_{j=n+1}^\infty \frac{(-4\pi^2 k^2)^j}{j!}||_2 \leq \epsilon$$
To that end, we use the bound for alternating series that $|\sum_{j=n+1}^\infty a_j| \leq |a_{n+1}|$. Hence,
$$|\hat{f}(k) \sum_{j=n+1}^\infty \frac{(-4\pi^2 k^2)^j}{j!}| \leq |\hat{f}(k)| \frac{(4\pi^2 k^2)^{n+1}}{(n+1)!}$$
It is well known that if a function $f$ is smooth then its fourier transform satisfies
$$|\hat{f}(k)| \leq \frac{C_m}{k^m}$$
for all $m > 0$ (see e.g. this thread). Using this estimate we can make the tail of the series arbitrarily small.
$$\int_T^\infty |\hat{f}(k)|^2 \left|\frac{(4\pi^2 k^2)^{n+1}}{(n+1)!}\right|^2 dk \leq
C_m^2 \int_T^\infty \left|\frac{(4\pi^2)^{2n+2} (k^{2n + 2 - 2m})}{(n+1)!}\right| dk$$
(This is the false step as is:) Using this, we can choose $N, T$ sufficiently large that
$$\int_T^\infty |\hat{f}(k)|^2 \left|\frac{(4\pi^2 k^2)^{n+1}}{(n+1)!}\right|^2 dk \leq \frac{\epsilon}{4}$$
for all $n \geq N$.
To finish the proof, we choose $N_1, T$ so that $\forall n \geq N_1$:
$$||(\hat{f}e^{-4\pi^2 k^2} - \hat{f}_n)\chi_{[-T, T]}||_2 < \frac{\epsilon}{2}$$
Using this and the bounds for the tail of the integral establish above we can show there exists $N_2 \geq N_1$ such that for all $n \geq N_2$
$$||\hat{f}e^{-4\pi^2 k^2} - \hat{f}_n||_2 \leq \epsilon$$
I have asked the community for assistance with this at this thread.