This was a major pain for me. I use two-finger scroll for vertical and horizontal scrolling. Chrome trips me up by occasionally (when I swipe fast enough) browsing through my page history. A big inconvenience especially when one is working on documents or forms online. Almost got to the point where I was thinking of swearing off Chrome altogether.
I looked online and found some forums which said that it couldn’t be done. Then I found this website which gives simple instructions to disable this on an application basis. Just run the following command in terminal:
defaults write com.google.Chrome.plist AppleEnableSwipeNavigateWithScrolls -bool FALSE
Update: This doesn’t seem to work in Mavericks. Chrome still has the same annoying behavior.