(I was going to leave @Matt L.'s answer but, given the line of comments, I'll try, too)
Let's say you have a 1st order lowpass prototype and you feed it a sine:
$$\begin{align}
&H(s)=\dfrac{1}{s+1} \tag{1} \\\\
&h(t)=u(t)\mathrm{e}^{-t} \tag{2} \\\\
&x(t)=u(t)\sin(t) \tag{3}
\end{align}$$
Applying the convolution integral you get the output to be (omitting the $u(t)$ for a clearer view):
$$y(t)=\dfrac{\mathrm{e}^{-t}+\sin(t)-\cos(t)}{2}=\dfrac{\mathrm{e}^{-t}}{2}+\cfrac{\sin\left(t-\dfrac{\pi}{4}\right)}{\sqrt2} \tag{4}$$
After the transient has decayed enough that its value doesn't influence the output enough ($5t$ or more), every time the input is zero (at every $n\pi/2$) the output will be:
$$y\left(n\dfrac{\pi}{2}\right)=\cfrac{\sin\left(n\dfrac{\pi}{2}-\dfrac{\pi}{4}\right)}{\sqrt2}$$
As long as the input stays as $\sin(t)$, that makes the output have alternating values $\pm 1/2$ for each input's zero crossing. What could you infer from this: that the output has infinite gain, that it creates something out of nothing? What will the transfer function be?
Conversely, every time the input is $\pm 1/\sqrt2$, the output will be zero. Would you say that the transfer function is zero?
This is why you can't rely on the time domain response in order to get the transfer function: all the results you'll get will vary from a fraction of a second to another.
And if you use a different frequency then you will get different results, each time, for each frequency. It is because of this that the Laplace transform is used (as long as it's an LTI, see @Matt L.'s answer): not only it converts from time domain into frequency domain thus, allowing us to determine the exact response of the system for each input, but it does so while managing to transform the difficult differential equations that govern the time domain into simple algebraic, linear equations, much easier to solve.
Note that this Laplace transform is nothing but a mathematical abstraction, it does not exist in the real world. It's a very useful tool to have but, in practice, even frequency response analyzers are oblivious to the existence of Laplace -- they do it by injecting a small signal with a swept frequency, then measuring the system for each of these frequencies. Then they collate the results and you get to see the frequency response. In practice. In theory, that's where you have the luxury of Laplace and we're ever so grateful for it.