Something like this should work as you want:
/jsonapi/user/user?filter[user-uid][condition][path]=uid&filter[user-uid][condition][operator]=NOT IN&filter[user-uid][condition][value][]=0&filter[user-uid][condition][value][]=1
For more informations: https://www.drupal.org/node/2943641
Edit: If you use cURL, brackets will throw an error, add "--globoff" to your request.
Example:
curl --globoff --location --request GET "{{localhost}}/jsonapi/node/article?sort=nid&page[limit]=10&filter[article-title][path]=title&filter[article-title][value]=headless&filter[article-title][operator]=NOT%20IN".
Reference: https://stackoverflow.com/a/8333999/5052969