So I just learned about Fourier transforms and I know that, if $f(x)$ is integrable and satisfies $\lim\limits_{|x|\rightarrow\infty}f(x)=0$ we have $\hat{\frac{\partial f}{\partial x_j}}(k)=2\pi ik_j\hat{f}(k)$. This can be used to obtain the so called fundamental solution to the heat equation $$\frac{\partial u}{\partial t}=\Delta u$$
where $\Delta$ denotes the laplacian, by applying this rule twice to the RHS, solving for the Fourier transform and retrieving $u$ through an inverse Fourier transform. My question is: how does one know that the solution to heat equation must disappear at infinity? Is this even true in general or is it just an imposed boundary condition?
You should ask your question at https://physics.stackexchange.com/ to get a discussion of physical reasons for choosing that boundary condition.
As for mathematical reasons... the Fourier transform is best behaved as an operator on $L^2$ functions; that is, functions for which $\int_{-\infty}^{\infty} |f(x)|^2 \, \mathrm{d} x \neq \infty$.
So, to use an argument involving Fourier transforms, it's nice to first restrict the problem to $L^2$ functions.
I strongly expect actual condition your source wanted is not $\lim_{|x| \to \infty} f(x) = 0$ — instead, one of the three following conditions that often arise in Fourier theory was actually intended:
and either you misinterpreted the source, the source was abusing notation, or the source is generally confused about what conditions it needs to apply.