The statement is true if and only if the right hand side acts like a density for $X+Y$; that is,
$$F_{X+Y}(a)=\mathbb{P}(X+Y\le a) = \int_{-\infty}^a f_{X+Y}(z)\,\mathrm{d}z = \int_{-\infty}^a \left(\int f_X(x) f_Y(z-x)\,\mathrm{d}x\right)\mathrm{d}z$$
for all $a$. Let's verify this by starting with the right hand side.
Apply Fubini's Theorem to change the order of integration and make the substitution $z = x+y$. The determinant of its Jacobian is $1$, so no additional terms are introduced by this change of variables. Note that because $z$ and $y$ are in one-to-one correspondence and $-\infty \lt z \le a$ if and only if $-\infty \lt y \lt a-x$, we may rewrite the integral as
$$=\int \left(\int_{-\infty}^{a-x}f_X(x)f_Y(y)\,\mathrm{d} y\right)\mathrm{d}x.$$
By definition this is the integral over $\mathbb{R}^2$ of
$$=\iint I(x+y\le a)f_X(x)f_Y(y)\,\mathrm{d}y\,\mathrm{d}x$$
where $I$ is the indicator function of a set. Finally, since $X$ and $Y$ are independent, $f_{(X,Y)}(x,y) = f_X(x)f_Y(y)$ for all $(x,y)$, revealing the integral as merely the expectation
$$=\iint I(x+y\le a)f_{(X,Y)}(x,y)\,\mathrm{d}y\,\mathrm{d}x = \mathbb{E}(I(X+Y\le a))=\mathbb{P}(X+Y\le a),$$
as desired.
More generally, even when one or both of $X$ or $Y$ does not have a distribution function, we can still obtain
$$F_{X+Y}(a) = \mathbb{E}_X\left(F_Y(a-X)\right) = \mathbb{E}_Y\left(F_X(a-Y)\right)$$
directly from basic definitions, using the expectation of indicators to go back and forth between probabilities and expectations and exploiting the independence assumption to break the calculation into separate expectations with respect to $X$ and $Y$:
$$\eqalign{
\mathbb{P}(X+Y\le a) &= \mathbb{E}(I(X+Y\le a)) \\
&= \mathbb{E}_X\left(\mathbb{E}_Y(I(X+Y\le a)\right) \\
&= \mathbb{E}_X\left(\mathbb{P}_Y(Y\le a-X)\right) \\
&=\mathbb{E}_X(F_Y(a-X)).
}$$
This includes the usual formulas for discrete random variables, for instance, albeit in a slightly different form than usual (because it is stated in terms of the CDFs rather than the probability mass functions).
If you have a strong enough theorem about interchanging derivatives and integrals, you can differentiate both sides with respect to $a$ to obtain the density $f_{X+Y}$ in one stroke,
$$\eqalign{
f_{X+Y}(a) &= \frac{\mathrm{d}}{\mathrm{d}a} F_{X+Y}(a) =\mathbb{E}_X\left(\frac{\mathrm{d}}{\mathrm{d}a} F_Y(a-X)\right) = \mathbb{E}_X \left(f_Y(a-X)\right) \\
&= \int f_X(x) f_Y(a-x) \,\mathrm{d} x.
}$$