I will attempt to atone for my previous error by showing something opposite -- that $\tilde{\Theta}\left(\frac{1}{\epsilon^2}\right)$ samples are sufficient (the lower bound of $1/\epsilon^2$ is almost tight)! See what you think....
The key intuition starts from two observations. First, in order for distributions to have an $L_2$ distance of $\epsilon$, there must be points with high probability ($\Omega(\epsilon^2)$). For example, if we had $1/\epsilon^3$ points of probability $\epsilon^3$, we'd have $\|D_1 - D_2\|_2 \leq \sqrt{\frac{1}{\epsilon^3} (\epsilon^3)^2} = \epsilon^{3/2} < \epsilon$.
Second, consider uniform distributions with an $L_2$ distance of $\epsilon$. If we had $O(1)$ points of probability $O(1)$, then they would each differ by $O(\epsilon)$ and $1/\epsilon^2$ samples would suffice. On the other hand, if we had $O(1/\epsilon^2)$ points, they would each need to differ by $O(\epsilon^2)$ and again $O(1/\epsilon^2)$ samples (a constant number per point) suffices. So we might hope that, among the high-probability points mentioned earlier, there is always some point differing "enough" that $O(1/\epsilon^2)$ draws distinguishes it.
Algorithm. Given $\epsilon$ and a confidence parameter $M$, let $X = M \log(1/\epsilon^2)$. Draw $\frac{X}{\epsilon^2}$ samples from each distribution. Let $a_i,b_i$ be the respective higher,lower number of samples for point $i$. If there is any point $i \in [n]$ for which $a_i \geq \frac{X}{8}$ and $a_i-b_i \geq \sqrt{a_i} \frac{\sqrt{X}}{4}$, declare the distributions different. Otherwise, declare them the same.
The correctness and confidence bounds ($1-e^{-\Omega(M)}$) depend on the following lemma which says that all of the deviation in $L_2$ distance comes from points whose probabilities differ by $\Omega(\epsilon^2)$.
Claim. Suppose $\|D_1 - D_2\|_2 \geq \epsilon$. Let $\delta_i = |D_1(i) - D_2(i)|$. Let $S_k = \{i : \delta_i > \frac{\epsilon^2}{k}\}$. Then
$$\sum_{i \in S_k} \delta_i^2 \geq \epsilon^2\left(1-\frac{2}{k}\right).$$
Proof. We have
$$ \sum_{i \in S_k} \delta_i^2 ~ + ~ \sum_{i \not\in S_k} \delta_i^2 \geq \epsilon^2. $$
Let us bound the second sum; we wish to maximize $\sum_{i \not\in S_k} \delta_i^2$ subject to $\sum_{i \not\in S_k} \delta_i \leq 2$. Since the function $x \mapsto x^2$ is strictly convex and increasing, we can increase the objective by taking any $\delta_i \geq \delta_j$ and increasing $\delta_i$ by $\gamma$ while decreasing $\delta_j$ by $\gamma$. Thus, the objective will be maximized with as many terms as possible at their maximum values, and the rest at $0$. The maximum value of each term is $\frac{\epsilon^2}{k}$, and there are at most $\frac{2k}{\epsilon^2}$ terms of this value (since they sum to at most $2$). So
$$ \sum_{i \not\in S_k} \delta_i^2 \leq \frac{2k}{\epsilon^2}\left(\frac{\epsilon^2}{k}\right)^2 = \frac{2\epsilon^2}{k} . ~~~~ \square $$
Claim. Let $p_i = \max\{D_1(i),D_2(i)\}$. If $\|D_1 - D_2\|_2 \geq \epsilon$, there exists at least one point $i \in [n]$ with $p_i > \frac{\epsilon^2}{4}$ and $\delta_i \geq \frac{\epsilon \sqrt{p_i}}{2}$.
Proof. First, all points in $S_k$ have $p_i \geq \delta_i > \frac{\epsilon^2}{k}$ by definition (and $S_k$ cannot be empty for $k > 2$ by the previous claim).
Second, because $\sum_i p_i \leq 2$, we have
$$ \sum_{i \in S_k} \delta_i^2 \geq \epsilon^2 \left(\frac{1}{2} - \frac{1}{k}\right) \sum_{i \in S_k} p_i, $$
or, rearranging,
$$ \sum_{i \in S_k} \left( \delta_i^2 - p_i \epsilon^2 \left(\frac{1}{2} - \frac{1}{k}\right)\right) \geq 0 , $$
so the inequality
$$ \delta_i^2 \geq p_i \epsilon^2 \left(\frac{1}{2} - \frac{1}{k}\right) $$
holds for at least one point in $S_k$. Now pick $k=4$. $\square$
Claim (false positives). If $D_1 = D_2$, our algorithm declares them different with probability at most $e^{-\Omega(M)}$.
Sketch. Consider two cases: $p_i < \epsilon^2/16$ and $p_i \geq \epsilon^2/16$. In the first case, the number of samples of $i$ will not exceed $X/8$ from either distribution: The mean number of samples is $< X/16$ and a tail bound says that with probability $e^{-\Omega(X/p_i)} = \epsilon^2 e^{-\Omega(M/p_i)}$, $i$'s samples do not exceed their mean by an additive $X/16$; if we are careful to keep the value $p_i$ in the tail bound, we can union bound over them no matter how many such points there are (intuitively, the bound decreases exponentially in the number of possible points).
In the case $p_i \geq \epsilon^2/16$, we can use a Chernoff bound: It says that, when we take $m$ samples and a point is drawn with probability $p$, the probability of differing from its mean $pm$ by $c \sqrt{pm}$ is at most $e^{-\Omega((c\sqrt{pm})^2/pm)} = e^{-\Omega(c^2)}$. Here, let $c = \frac{\sqrt{X}}{16}$, so the probability is bounded by $e^{-\Omega(X)} = \epsilon^2 e^{-\Omega(M)}$.
So with probability $1-\epsilon^2e^{-\Omega(M)}$, (for both distributions) the number of samples of $i$ is within $\sqrt{p_i\frac{X}{\epsilon^2}}\frac{\sqrt{X}}{16}$ of its mean $p_i\frac{X}{\epsilon^2}$. Thus, our test will not catch these points (they are very close to each other), and we can union bound over all $16/\epsilon^2$ of them. $\square$
Claim (false negatives). If $\|D_1 - D_2\|_2 \geq \epsilon$, our algorithm declares them identical with probability at most $\epsilon^2 e^{-\Omega(M)}$.
Sketch. There is some point $i$ with $p_i > \epsilon^2/4$ and $\delta_i \geq \epsilon \sqrt{p_i}/2$. The same Chernoff bound as in the previous claim says that with probability $1-\epsilon^2 e^{-\Omega(M)}$, the number of samples of $i$ differs from its mean $p_i m$ by at most $\sqrt{p_i m} \frac{\sqrt{X}}{16}$. That is for (WLOG) distribution $1$ which has $p_i = D_1(i) = D_2(i) + \delta_i$; but there is an even lower probability of the number of samples of $i$ from distribution $2$ differing from its mean by this additive amount (as the mean and variance are lower).
So with high probability the number of samples of $i$ from each distribution is within $\sqrt{\frac{p_i X}{\epsilon^2}} \frac{\sqrt{X}}{16}$ of its mean; but their probabilities differ by $\delta_i$, so their means differ by
$$ \frac{X}{\epsilon^2}\delta_i \geq \frac{X \sqrt{p_i}}{2\epsilon} = \sqrt{\frac{p_i X}{\epsilon^2}} \frac{\sqrt{X}}{2} . $$
So with high probability, for point $i$, the number of samples differs by at least $\sqrt{\# samples(1)} \frac{\sqrt{X}}{4}$. $\square$
To complete the sketches, we would need to more rigorously show that, for $M$ big enough, the number of samples of $i$ is close enough to its mean that, when the algorithm uses $\sqrt{\# samples}$ rather than $\sqrt{mean}$, it doesn't change anything (which should be straightforward by leaving some wiggle room in the constants).