I think you may have been looking at it too long. I see what you mean, but a comma doesn't add anything. My suggestion is to either simply italicize newItem as in:

Replaces the existing item associated with the provided key with newItem.

or change it to something like:

Replaces the provided key's currently-associated item with newItem.

I think you may have been looking at it too long. I see what you mean, but a comma doesn't add anything. My suggestion is to either simply italicize newItem as in:

Replaces the existing item associated with the provided key with newItem.

or change it to something like:

Replaces the provided key's currently associated item with newItem.