No. Both proposal are incorrect. The right sentence is :
Je ne vous comprends pas.

But be careful:

• When a stranger say “Je ne vous comprends pas”, we understand he don’t understand French. (I don’t understand what you say)
• When a French say “Je ne vous comprends pas” to another French, it more generally means “I do not understand YOU”, i.e. I disagree with you.

Now why vous is between ne and vous … I don’t know, I just speak like my mother teach me !

As you’ve been told “Je ne comprends pas vous” is grammatically incorrect.
You’re also mistaking if you think that le pronom vous in the sentence “Je ne vous comprends pas” isn’t un complément d’objet direct. It is.
– Je ne comprends pas Pierre.
Pierre is a groupe nominal when used as a complément d’objet direct, it is placed after the verb.
– Je ne le comprends pas.
Le is a pronom personnel complément when used as a complément d’objet direct, it is placed before the verb .
Both of them are complément d’objet direct.

Same goes for a complément d’objet indirect.
– Je souris à Pierre.
– Je lui souris.

Les compléments d’objet are functions. They have a grammatical role.
Les pronoms are words. They are regulated by grammar.
It doesn’t make sense to ask if a function can replace a word. Functions act on words.