Dock - Remove spacer? Is there a way to remove the spacer between the downloads stack and apps?
As far as I know, this is not possible through normal means. And by that I mean I doubt you could change this without hacking the OS.

I know you can add spaces:

Adjust width of spacer between Mac OS dock icons

defaults write com.apple.dock persistent-apps -array-add '{"tile-type"="small-spacer-tile";}' &amp;&amp; killall Dock


or 

defaults write com.apple.dock persistent-apps -array-add '{"tile-type"="spacer-tile";}'


Those are the only space customizations I am aware of.

I know this is not the answer you were hoping for but I believe it to be the correct answer.