Apple has introduced the possibility of deleting an app. Quoting the iTunes Connect guide:
If you have created an app in iTunes Connect that you no
Follow Below Steps
Login into your iTunes Connect with your developer id: https://itunesconnect.apple.com
Click on App Icon
Click on Rights And Pricing
At the bottom This app will be on sale in all App Stores worldwide. Or, you can select specific stores “here”. Click on here button to open all specific app stores.
Click on the “Deselect All” button to uncheck all App Store territories.
Click on “Save Changes” button.
Now when you save all these and go to back to your App icon home screen. There will be one more button appear “Delete Application” after “Set Up iAd Network”.
Click on Delete button and read instructions.
Your app will disappear from the app store within 24 hours.
You could reuse the App Name of the app you have deleted if you change the Default Language of the application information.
Full details here: http://hesh.am/2012/01/recovering-a-deleted-app-name-in-itunes-connect/
It's possible to salvage the situation. I also made a mistake and forgot to type com.XX part when entering the Bundle ID. My app was not live yet, but once you submit BundleID, it's not possible to change it.
What you can change though, is the "App Name". Thus:
when you delete an application from iTunes Connect you can't upload with the same App Name and SKU in the same developer Apple id. This resource is for migrate an App for another company or individual developer. Ex. when an App was sold.
Simple steps for Deleting/Removing app from iTunes Connect:
iTunesConnect>App>Rights and Pricing>specific stores> Deselect All> Save
Change app status: Developer Removed From Sale
After 24hours app will be removed.
Please see Removing an App From Sale (page 92) section on iTunes Connect Developer Guide 6.3
After removing all assigned territory checkboxes from your app in the Rights and Pricing section,, the status changes to Developer Removed from Sale and your app will not be seen on the App Store within 24 hours.