The El Capitan way

Since OS X 10.11 (El Capitan) the setting is system wide, and Chrome respects that as you can see in this Chrome bug report.

To change it, go in System Preferences > Trackpad > More Gestures and untick “Swipe Between Pages”.

The old, pre-El Capitan way

Before El Capitan Chrome had its own setting, which you could change by typing the following commands in Terminal

defaults write com.google.Chrome.plist AppleEnableSwipeNavigateWithScrolls -bool FALSE
defaults write com.google.Chromium.plist AppleEnableSwipeNavigateWithScrolls -bool FALSE
defaults write com.google.ChromeCanary.plist AppleEnableSwipeNavigateWithScrolls -bool FALSE