Delete them from your device and then do an iCloud backup. You may also be able to do it via iCloud.com but I'm not sure. All of my contacts on my device aren't on my iCloud.com so that may not be the best way to do it.
Great question! Have the contacts been deleted from the device as well?
_VZW Follow us on TWITTER @VZWSupport If my response answered your question please click the Correct Answer button under my response. This ensures others can benefit from our conversation. Thanks in advance for your help with this!!