i don't think there is an API call to do that, but you could do it with a few steps:
-
get the list of fields in the index pattern with:
http://localhost:5601/api/index_patterns/_fields_for_wildcard?pattern=NAME_OF_YOUR_INDEX&meta_fields=["_source","_id","_type","_index","_score"]
, -
escape returned json and update the index with:
curl 'http://localhost:5601/api/saved_objects/index-pattern/ID_OF_YOUR_INDEX' -X PUT -H 'Content-Type: application/json' -H "kbn-xsrf: true" --data-binary '{"attributes":{"title":"NAME_OF_YOUR_INDEX","fields":"[ESCAPED_JSON_WITH_LIST_OF_YOUR_FIELDS]"}}'
(take a look at network panel in chrome when you click the refresh fields button)