I leave here what John Mu told about the Penguin update in a Hangout made in October 19, 2012, where he says that we must wait next update...:
Question:…Is the disavow tool good to remove [a] Penguin penalty from a domain?
John Mueller: So, generally speaking, the Penguin algorithm is a webspam algorithm that can also take into account links like that, so if you use the disavow tool that would be similar to adding a nofollow to those links which would take those out of the way that we process those links from an algorithmic point of view. So, with that in mind if the Penguin algorithm has been picking up those links for your site and kind of using those appropriately, then using the disavow tool will take those out of the use by the Penguin algorithm.
So, that should work.
But again, this is something that is a little bit, I guess, advanced, where you really have to watch what you are doing there. Most websites shouldn’t need to use this tool and you should also keep in mind that it takes quite a bit of time for this to update. So on the one hand we have to recrawl those links and on the other hand we have to update the Penguin algorithm data as well…so, it’s something where you wouldn’t see a change from one day to the next.