What you need to do is this.
- Go to “Manage Your Applications” and select the app.
- Click “Rights and Pricing” (blue button at the top right.
- Below the availability date and price tier section, you should see a grid of checkboxes for the various countries your app is available in. Click the blue “Deselect All” button.
- Click “Save Changes” at the bottom.
Your app’s state will then be “Developer Removed From Sale”, and it will no longer be available on the App Store in any country.