A space being perfect or not depends only on the topology of the space, while the closure property (the closure of the open ball $B_r(x) = \{ y : d(x,y) < r\}$ is the closed ball $K_r(x) = \{ y : d(x,y) \leqslant r\}$ for all $r \in (0,+\infty)$ and all $x \in X$) clearly depends on the metric. On every metric space $(X,d)$ with at least two points we can find an equivalent metric (i.e. a metric $d'$ inducing the same topology as $d$) such that there is at least one open ball $B_r(x)$ whose closure is a proper subset of $K_r(x)$. A uniform construction works. There always is a point $x_0 \in X$ and a $c > 0$ such that $B_c(x_0)$ is not dense in $X$, and there is a $y \in X$ with $d(x_0,y) = c$. Then taking $d'(x,y) = \min \{ c, d(x,y)\}$ works.
Hence a perfect metric space need not have the closure property.
Conversely, the closure property implies that the space is perfect if the space is not a singleton space.
This is vacuously true for the empty space. If the space contains more than one point, choose an arbitrary $x \in X$, and $y \in X \setminus \{x\}$. Let $r = d(x,y)$. Then by the closure property $x \in \overline{B_r(y)}$, hence for all $\varepsilon > 0$ we have $B_r(y) \cap B_{\varepsilon}(x) \neq \varnothing$. Since $x \notin B_r(y)$ it follows that $B_{\varepsilon}(x) \setminus \{x\} \neq \varnothing$. Hence $x \in X'$. Since $x$ was arbitrary, $X$ is perfect.
Singleton spaces aren't perfect, but they trivially have the closure property.