In the template anatomy, you cant set stack-level tags directly. However you can create a wrapper template, having a single resource of AWS::CloudFormation::Stack.
You can define stack-level tags on that resource:
{
  "AWSTemplateFormatVersion": "2010-09-09",
  "Description": "WrapperTemplate",
  "Resources": {
    "WrappedStackWithStackLevelTags": {
      "Type" : "AWS::CloudFormation::Stack",
      "Properties" : {
        "Tags" : [ { "Key" : "Stage", "Value" : "QA" } ],
        "TemplateURL" : "your-original-template-s3-url"
      }
    }
  }
}