EDIT: I for to mention that you need to generate your own document_id and set that. So in order to update a existing document you need to set a id on the initial document and reuse that. (bad example: ie: email_address) or query ES for the document_id using the logstash-filter-elasticsearch plugin.
It will look something like this.
output {
elasticsearch {
host => 'your es host'
action => 'update'
document_id => 'your generated document id'
index => 'your index name
}
}