How can I filter nodes by term (entity reference) with jsonapi?
You were close, but your syntax was off. This is documented further down in your linked page, in the Filter Examples &gt; Get nodes by a value of a entity reference section.
SHORT
filter[uid.id][value]=BB09E2CD-9487-44BC-B219-3DC03D6820CD

NORMAL
filter[author-filter][condition][path]=uid.id
filter[author-filter][condition][value]=BB09E2CD-9487-44BC-B219-3DC03D6820CD

So, in your example, you'd need to use:
SHORT
/jsonapi/node/my_content_type?filter[field_ref_term.id][value]=f9c171db-1a1d-4d9a-bb55-5b0f8b033749

LONG
/jsonapi/node/my_content_type?filter[term-filter][condition][path]=field_ref_term.id&amp;filter[term-filter][condition][value]=f9c171db-1a1d-4d9a-bb55-5b0f8b033749