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Like on the right side of the following image:

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I don't use El Capitan, but it should be the same as in previous versions.

  1. In Finder menu bar: Go → Go to folder…
    • Insert this path: /System/Library/CoreServices/Dock.app/Contents/Resources/
  2. Search for: "dockbackground"

  3. Now, what file it is that you need to modify depends on a few things:

    • If you have Retina Mac, it's one of the @2x.png files
    • If you have System Preferences → General → ☑︎ Use dark menu bar and Dock checked, it's going to be one of the files with "dark" in the name.
  4. In this case, since you want to remove the border, you can just move all these files to another location.

    • Admin password required.
  5. The changes take effect next time the dock loads. You can force it to reload a few ways:
    • If using Terminal is not for you, you can just log out and log back in.
    • OR if you don't mind using Terminal, the quickest way is to open Terminal.app and run: killall -kill Dock (The dock will go into hiding and come back almost immediately with the changes)

If you want the old borders back, you can just move the files back to the folder.

  • Make sure you mention that you have to turn off SIP for this to work. – Arc676 Dec 8 '15 at 13:57
  • @Arc676 Forgot about that. I guess I would rather advice to downgrade to Yosemite :) – Joonas Dec 8 '15 at 13:57
  • @Joonas thanks for help, but every time I try to move dockbackgrounddark@2x.png to another folder, I get a message saying: ""dockbackgrounddark@2x.png" can’t be modified or deleted because it’s required by Mac OS X." – kirion Dec 9 '15 at 14:32
  • That would be the SIP talking, @kirion. Many people are choosing not to update for now, due to the crippling effect that it can have. I personally have so many 3rd party apps that would require me to disable SIP, that I haven't even put any thought into it yet. All the devs of affected applications have written about disabling it and why it's required. Here's the SIP article about TotalFinder as an example. – Joonas Dec 9 '15 at 20:33
  • Some devs are coming out with new versions, that work within the restrictions of SIP: Bartender, Default folder x. If I were in your shoes, and this is the only modification you want. I would just leave the dock border as it is. That said, I'm pretty sure you could disable SIP, make this modification and then turn it back on. – Joonas Dec 9 '15 at 20:34

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