South African Gavin Van den Berg played twice for Spain, but his eligibility was questioned by rival Romania, with World Rugby deciding he did not fit the criteria.
To qualify on residency rules, players involved in qualifying needed to have lived in their chosen country for 36 consecutive months.
Spain has pinned the blame on an alleged forgery of Van den Berg's passport.
World Rugby said in a statement that it had imposed a 10-point deduction from Spain's qualifying points total in European qualifying, also imposing a £25,000 fine and triggering a suspended £50,000 punishment that dated back to the 2019 Rugby World Cup qualifiers and related to another ineligibility case.
Spain can appeal against the punishment, but barring a successful challenge their place at the tournament in France will go to Romania, who will face South Africa, Ireland, Scotland and an Asia/Pacific qualifying team.
The Spanish Rugby Federation said in a statement: "As this very harsh sanction occurs as a result of an alleged forgery of the aforementioned player's passport, the Spanish Rugby Federation (FER) continues with the extraordinary disciplinary procedure initiated at the time and will shortly call a press conference to offer all the explanations that are required."