Yes, it does!
First, fix an element $\omega\in\Omega$.
Then every proper chain has length at most countably infinite:
$$\Omega\supsetneq E_1\supsetneq E_2\supsetneq\ldots\quad\omega\in E_k\in\Sigma$$
and therefore admits a lower bound:
$$\omega\in\bigcap_{k=1}^\infty E_k\in\Sigma$$
Hence, there is a minimal element by Zorn's lemma:
$$\omega\in A_\omega\in\Sigma$$
Now, consider distinct elements $\omega\neq\omega'$.
Assume $A_\omega\cap A_{\omega'}\neq\varnothing$ and $A_\omega\neq A_{\omega'}$.
Also either $\omega\in A_\omega\cap A_{\omega'}$ or $\omega\in A_\omega\cap A_{\omega'}^c$.
So w.l.o.g. $A_\omega\supsetneq A_\omega\cap A_{\omega'}$ with $\omega\in A_\omega\cap A_{\omega'}\in\Sigma$.
But that contradicts minimality.
Concluding, there is a finest measurable partition modulo repetitions:
$$\Omega=\bigsqcup_{\omega\in\Omega}A_\omega\quad A_\omega\in\Sigma$$
Especially, it is countable!