You really just need that if $\hat f ∈ \ell ^2$ then the function defined by $f:=\sum_{k∈\mathbb Z}\hat f_k E_k$ is a well defined $L^2$ function on $\Bbb T$ with Fourier transform $\hat f$. That is, the isometry between $\ell^2$ and $L^2$ is a two-way street: given an $L^2$ function, we have an $\ell^2$ sequence, and vice-versa.
In some detail, for any sequence with the suggestive name $\hat f ∈ \ell^2$, we can define a function $f:=\sum_{k∈ \Bbb Z} \hat f_k E_k ∈ L^2(\Bbb T)$, where $E_k$ are the Fourier basis. By orthogonality of $E_k$, $‖f‖^2_{L^2(\Bbb T)} = \sum |\hat f_k|^2 = ‖\hat f‖^2_{\ell^2} $. Also, if $\mathcal F:L^2 → \ell^2$ is the Fourier Transform then an easy check that for this particular $f$ defined above, we can recover $\hat f= \mathcal F f $.
Response to comments in reverse order -
The series converges in the $L^2$ sense; some work is hidden behind the words 'well-defined'. One needs to first check that $
\{ ∑_{|k|<N} \hat f_k E_k \}_{N\geq 0}$ is Cauchy in the $L^2$ norm; as $L^2$ is complete, there is a limit and we are free to define $$f:=\lim_{N→∞,\ L^2} \sum_{|k|<N} \hat f_k E_k$$
The $f$ I defined coincides with the sum purely by its definition; I suppose you mean to ask if you start with $f ∈ L^2$ and create $\mathcal F f ∈ \ell^2$, then how do we know that $f = ∑_{k∈ \Bbb Z} (\mathcal F f)_k E_k$? This is exactly because $E_k$ form an orthogonal basis, so that $⟨ f, E_k ⟩ =0 $ for every $k$ implies $f=0$.
A proof of this fact is based on the Weierstrass approximation theorem, which says that continuous functions $C$ on the circle can be uniformly approximated by (finite) trigonometric polynomials $\{ ∑_{|k|≤n}a_k E_k : a_k ∈ \Bbb R,\ n = 0,1,2,…\}$. [the version on a closed interval implies the version on the circle by mapping $[0,2\pi]→ \Bbb T$ with $E_1(x) = e^{ix}$.]
At the same time, $L^2$ is the completion of $C$ under the $L^2$ norm. So if we approximate $f ∈ L^2$ by a continuous periodic $g ∈ C(\Bbb T)$, and approximate $g$ uniformly by a finite trigonometric polynomial $g_N$,
we obtain with careful $ε$ management,
$$ ‖f - g_N ‖_{L^2} ≤ ‖f - g‖_{L^2} + ‖g - g_N‖_{L^2} < ε $$
By the hypothesis $0 = ∑_{k=-N}^N ⟨f,E_k⟩ E_k$. But also, this sum defines the orthogonal projection i.e. closest point (in $L^2$ distance) to $f$ in $\operatorname{span} \{E_{-N},…,E_{N}\}$. Hence $$‖f-0‖_{L^2} ≤ ‖f - g_N ‖_{L^2} ≤ ε $$
Since $ε>0$ was arbitrary, $f = 0$.
If we now apply this result to $f -\sum_{k∈\Bbb Z} (\mathcal F f)_k E_k$, the result follows.