AWS CLI で JSON を入力に与えてオプションも指定するとオプションが優先されるようです。

前提

aws-cli/1.14.8 Python/2.7.5 Linux/4.9.76-38.79.amzn2.x86_64 botocore/1.8.12

実行結果

$ cat create-db-instance.json
{
    "DBInstanceIdentifier": "test-aurora",
    "DBInstanceClass": "db.t2.small",
    "Engine": "aurora-mysql",
    "PubliclyAccessible": false,
    "DBClusterIdentifier": "test-aurora-cluster",
    "CopyTagsToSnapshot": true
}

$ aws rds create-db-instance --cli-input-json file://create-db-instance.json --db-instance-identifier override
{
    "DBInstance": {
......
        "DbInstancePort": 0,
        "DBInstanceIdentifier": "override"
    }