After a few googling, I've found out this simple solution. Thanks to Baryon from MacRumors Forums.
- Go to Applications folder, Right click on Skype, Choose Move to Trash.
- In my case, both Skype icons are gone from Launchpad. If you still see Skype icon in your Launchpad, click on it (Choose Yes when it ask you if you want to remove it).
- Go to Trash, right click on Skype, Choose Put Back.
That's it, only one Skype icon show up in my Launchpad now. Your mileage may vary, feel free to post it in comments.