[guided]Subtracting the two expansions and grouping by type of term:
\begin{align*}
\left[\frac{\partial}{\partial \bar z_k},\, \delta_j^\varphi\right] u
= \underbrace{\left(\frac{\partial}{\partial \bar z_k}\frac{\partial u}{\partial z_j} - \frac{\partial}{\partial z_j}\frac{\partial u}{\partial \bar z_k}\right)}_{(\mathrm{I})\ \text{second order}} \;\underbrace{-\ \left(\frac{\partial \varphi_{z_j}}{\partial \bar z_k}\right) u}_{(\mathrm{II})\ \text{survivor}} \;+\; \underbrace{\left(-\varphi_{z_j}\frac{\partial u}{\partial \bar z_k} + \varphi_{z_j}\frac{\partial u}{\partial \bar z_k}\right)}_{(\mathrm{III})\ \text{first order}}.
\end{align*}
We dispose of the three groups in turn.
Group $(\mathrm{III})$ is the easiest: the two first-order terms are literally identical and appear with opposite signs, so they cancel algebraically with no hypothesis needed. This is the payoff of having noted, at the end of the last step, that $\varphi_{z_j}\partial_{\bar z_k}u$ occurs in both expansions.
Group $(\mathrm{I})$ asks: do the Wirtinger operators commute on $u$? Why should they? Because they are constant-coefficient combinations of the real partials $\partial_{x_i}, \partial_{y_i}$, and $u$ is smooth — in particular $u \in C^2(\Omega)$, the exact regularity required by the [Symmetry of Second Derivatives](/theorems/332). That theorem says the real mixed second partials $\partial_{x_i}\partial_{x_\ell}u$, $\partial_{x_i}\partial_{y_\ell}u$, etc., are symmetric in the order of differentiation. Expanding $\partial_{\bar z_k}\partial_{z_j}u$ and $\partial_{z_j}\partial_{\bar z_k}u$ into real partials, the two expansions involve the same real second derivatives of $u$ in opposite orders and with the same constant coefficients; symmetry makes them equal:
\begin{align*}
\frac{\partial}{\partial \bar z_k}\frac{\partial u}{\partial z_j} = \frac{\partial}{\partial z_j}\frac{\partial u}{\partial \bar z_k}.
\end{align*}
So $(\mathrm{I})$ vanishes. (If $u$ were merely $C^1$ this could fail — but $u$ is smooth, so there is no obstruction.)
Group $(\mathrm{II})$ is the heart of the matter, and the only place the hypothesis on $\varphi$ is consumed. We must identify $\partial_{\bar z_k}\varphi_{z_j}$ with the Levi-form entry $\varphi_{j\bar k} = \partial_{z_j}\partial_{\bar z_k}\varphi$. As written, the derivatives sit in the order "$\partial_{\bar z_k}$ after $\partial_{z_j}$"; the definition of $\varphi_{j\bar k}$ has them in the order "$\partial_{z_j}$ after $\partial_{\bar z_k}$". To swap them we again invoke the [Symmetry of Second Derivatives](/theorems/332), now applied to $\varphi$. Its hypothesis is precisely $\varphi \in C^2(\Omega)$ — which is given — and we use the same reduction to real partials as for $u$:
\begin{align*}
\frac{\partial \varphi_{z_j}}{\partial \bar z_k} = \frac{\partial}{\partial \bar z_k}\frac{\partial \varphi}{\partial z_j} = \frac{\partial}{\partial z_j}\frac{\partial \varphi}{\partial \bar z_k} = \frac{\partial^2 \varphi}{\partial z_j\, \partial \bar z_k} = \varphi_{j\bar k}.
\end{align*}
Had $\varphi$ been only $C^1$, this second derivative would not even exist; had it been $C^2$ but with a non-symmetric pathology, the swap would fail — so $C^2$ is exactly what makes group $(\mathrm{II})$ a single well-defined number times $u$.
Collecting $(\mathrm{I}) = 0$, $(\mathrm{III}) = 0$, and $(\mathrm{II}) = -\varphi_{j\bar k}u$:
\begin{align*}
\left[\frac{\partial}{\partial \bar z_k},\, \delta_j^\varphi\right] u = -\,\varphi_{j\bar k}\, u.
\end{align*}[/guided]