I got a hole about the same size in just about the same spot on my 2006 after it was about a year old. I went to the auto parts store and spent $9.99 on a vinyl repair kit. It came with 12 different colors and 6 different textures. I only need black and smooth. I took it home and experimented on an old kitchen chair. I followed the directions clearly and it came out pretty good so I gave it a try on the seat and it came out even better (you've really got to follow the instructions, but it was fairly simple).
I was happy with the way it turned out, and was confident if I had any more vinyl repairs I was equipped to handle them. If you knew where the spot was and zeroed in on it you could tell there was a little dab of something, but otherwise it was unnoticeable. It held up until I traded the bike in at the dealer for my 2009.
One last bit of advice, when following the instructions, dont get aggressive and think if a little will work, a little more will work even better or you'll end up with a noticeable lump that you will have to remove and do a larger repair. The instructions are pretty clear and easy to follow.
Good luck! I know you can do it, and I'm certain you will be happy.