Brookes was the only rider in the top 19 to lap slower on Saturday, but still hung on to pole until Parkes barged ahead on his very last lap.
Third on the grid went to Fabien Foret followed by local star Massimo Roccoli, who made it three Yamahas on the front row.
Rookie Jonathan Rea heads row two, while world championship leader Joan Lascorz was only 16th fastest.
Meanwhile, Craig Jones qualified a painful twelfth after fracturing his hand during morning practice.
"The mobile clinic patched me up pretty well but even then I had to really bite the screen and give it all I could to put in a fast lap – it was extremely painful," said the Briton, who has taken two third positions so far this year. "It is my clutch hand which is a small mercy because if it had been my throttle hand it would have been much worse.
"My Parkalgar Honda has been brilliant this weekend and its high top speed certainly helped me make a good lap. Thank you to my team for the bike and also for fixing my number one CBR600 between sessions so I could use my quickest machine in qualifying.
"With such a quick bike I think I'll make up places tomorrow in the race; realistically, the top ten would be good but I'll be trying for higher and top five if possible," he added.
WSS final qualifying - top 10:
1. Parkes (Yamaha)
2. Brookes (Honda) +0.466secs
3. Foret (Yamaha) +0.552secs
4. Roccoli (Yamaha) +0.665secs
5. Rea (Honda) +0.879secs
6. Vizziello (Honda) +0.932secs
7. Pitt (Honda) +0.955secs
8. Harms (Honda) +1.101secs
9. Lagrive (Honda) +1.117secs
10. Aitchison (Triumph) +1.136secs
12. Jones (Honda) +1.428secs
20. Walker (Kawasaki) +2.246secs
27. Gowland (Honda) +3.207secs
29. Coghlan (Honda) +3.409secs
