If you change the setting for auto-update in the Playstore app, this affects only apps you install thereafter (it's the default to set on installation of new apps). If you don't want your already installed apps to auto-update, you've got to check with each of them:
- Open the Playstore app
- Navigate to "My Apps" (via the "Hamburger menu")
- Open the settings for each app you don't want to auto-update, and uncheck the auto-update setting
Auto-update check box (click images for larger variants)
Also see this howto for a complete walk-through with screenshots (second screenshot above comes from there). Location and "visuals" of that check-box might depend on the version of the playstore app, but the principle should stay the same.
Note that for some "system apps" (usually parts of the "Google Apps") you might not be able to turn this off. I've e.g. experienced that for Google Play Services on some devices.