document_id => に任意の値を設定でOK

output {
    elasticsearch { 
        document_id => "%{some_id_field}"
    }
}

実際の設定は以下のような感じになる

output {
  elasticsearch {
    document_id => "%{some_id_field}" # _IDをsome_id_fieldとする
    hosts => ["http://elasticsearch:9200/"]
    user => "elastic"
    password => "xxxxx"
    index => "some_index"
    ...
  }
}

参考

How does logstash generate '_id' when the outputting to elastic search? - Elastic Stack / Logstash - Discuss the Elastic Stack