[guided]We begin with an arbitrary formula, because equality of complete types means agreement on every formula over the parameter set. Thus fix $m \in \mathbb{N}$, an $L$-formula
\begin{align*}
\varphi(x_1,\dots,x_n,y_1,\dots,y_m),
\end{align*}
and a parameter tuple $a=(a_1,\dots,a_m) \in A^m$. The tuple $i_M(a)=(i_M(a_1),\dots,i_M(a_m))$ is the interpretation of these parameters in $M$, and $i_N(a)=(i_N(a_1),\dots,i_N(a_m))$ is the corresponding interpretation in $N$.
The key point is that quantifier elimination is applied before substituting parameters. Since $T$ has quantifier elimination, there is a quantifier-free $L$-formula
\begin{align*}
\psi(x_1,\dots,x_n,y_1,\dots,y_m)
\end{align*}
with the same free variables as $\varphi$ such that $T$ proves their universal equivalence:
\begin{align*}
T \models \forall x_1 \cdots \forall x_n \forall y_1 \cdots \forall y_m \bigl(\varphi(x_1,\dots,x_n,y_1,\dots,y_m) \leftrightarrow \psi(x_1,\dots,x_n,y_1,\dots,y_m)\bigr).
\end{align*}
This uniformity matters: the same quantifier-free formula $\psi$ works for every possible substitution of the parameter variables $y_1,\dots,y_m$.
Now use that both structures are models of $T$. Since $M \models T$, the displayed equivalence is true in $M$, and substituting $b \in M^n$ for the variables $x_1,\dots,x_n$ and $i_M(a) \in M^m$ for the variables $y_1,\dots,y_m$ gives
\begin{align*}
M \models \varphi(b,i_M(a)) \quad \Longleftrightarrow \quad M \models \psi(b,i_M(a)).
\end{align*}
Likewise, since $N \models T$, substituting $c \in N^n$ and $i_N(a) \in N^m$ gives
\begin{align*}
N \models \varphi(c,i_N(a)) \quad \Longleftrightarrow \quad N \models \psi(c,i_N(a)).
\end{align*}
Thus the original formula has been reduced, in both models and for the same parameter tuple, to the quantifier-free formula $\psi$.[/guided]