Here is a more elementary proof which uses only parity of the Yukawa theory and Lorentz-invariance and does not use the concept of the effective action.
The correlation function is
$\Gamma(t_1,\vec{r}_1,t_2,\vec{r}_2,t_3,\vec{r}_3) = \langle \mathrm{T} \phi(t_1, \vec{r}_1),\phi(t_1, \vec{r}_1), \phi(t_1, \vec{r}_1)\rangle$. Let me consider the Fourier image of the correlation function $\Gamma(\omega_1, \vec{p}_1, \omega_2, \vec{p}_2, -\omega_1-\omega_2, -\vec{p}_1 - \vec{p}_2)$ and send the three-momentum $\vec{p}_1 + \vec{p}_2$ to zero with a Lorentz transformation. The correlation function now takes form $\Gamma(\omega_1', \vec{p}', \omega_2', -\vec{p}', -\omega_1'-\omega_2', 0)$.
The parity transform changes the sign of $\Gamma$ and the signs of entering 3-momenta. On the other hand, it is possible to perform a rotation which transforms
$\vec{p}'$ into $-\vec{p}'$. So,
\begin{equation}
\begin{cases}
\Gamma(\omega_1', \vec{p}', \omega_2', -\vec{p}', -\omega_1'-\omega_2', 0) = -\Gamma(\omega_1', -\vec{p}', \omega_2', \vec{p}', -\omega_1'-\omega_2', 0) & \mathrm{(parity)}\\
\Gamma(\omega_1', \vec{p}', \omega_2', -\vec{p}', -\omega_1'-\omega_2', 0) = \Gamma(\omega_1', -\vec{p}', \omega_2', \vec{p}', -\omega_1'-\omega_2', 0) & \mathrm{(rotation\,\, invariance)}
\end{cases}
\end{equation}
Therefore, $\Gamma$ is zero for all possible values of 4-momenta.