[guided]The role of quantifier elimination is to remove the only part of a formula that might not be visibly respected by an arbitrary embedding: the existential and universal quantifiers. The cited theorem says that, modulo $\operatorname{ACF}_p$, every formula is equivalent to one with no quantifiers.
More precisely, for the fixed formula $\varphi(x_1,\dots,x_n,y_1,\dots,y_m)$, quantifier elimination gives a quantifier-free formula $\psi(x_1,\dots,x_n,y_1,\dots,y_m)$ satisfying
\begin{align*}
\operatorname{ACF}_p \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*}
The hypotheses needed to use this result are exactly that $K$ and $L$ are algebraically closed fields of characteristic $p$, so both are models of $\operatorname{ACF}_p$. Hence the displayed equivalence holds inside both structures. Evaluating it at $b,a$ in $K$ and at $\iota(b),\iota(a)$ in $L$ gives
\begin{align*}
K \models \varphi(b,a)
&\Longleftrightarrow
K \models \psi(b,a), \\
L \models \varphi(\iota(b),\iota(a))
&\Longleftrightarrow
L \models \psi(\iota(b),\iota(a)).
\end{align*}
Thus the original problem has been reduced to the quantifier-free case. This reduction is the point where algebraic closedness is used: arbitrary fields do not admit this quantifier-elimination reduction in the ring language.[/guided]