Tuesday's announcement is not the only controversy to surround the Championship, after five Spain players were banned for a combined total of 121 weeks for their furious reaction to Romanian referee Vlad Iordachescu's handling of their crucial clash with Belgium.
World Rugby said in a press release that in line with the decision of an independent disputes committee, "Russia will qualify for Rugby World Cup 2019 as Europe 1, joining Ireland, Scotland, Japan and the playoff victor in Pool A, while Germany will progress to the European playoff with Portugal, subject to the appeals process".
Each team has been deducted five championship points for every game an ineligible player was used (40-point deduction for Spain and a 30-point deduction for both Belgium and Romania), meaning Russian Federation now qualifies for the World Cup in place of Romania.
Spain and Belgium have also been retrospectively penalised for the same reason.
Germany, who have never been in a World Cup, now have another chance as they are promoted to face Portugal in a playoff, though the winners face a daunting final step with a two-legged playoff against Samoa.
The European qualifying tournament was thrown into disarray when Spain lost 18-12 in their final game to Belgium, having only needed a win to qualify for Japan.
The victor on aggregate will qualify for Pool A, while the loser will progress to the repechage competition in November.
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Spain used Mathieu Belie and Bastien Fuster, who have both previously played for France Under-20s, in eight qualification matches, leading to a 40-point deduction and a 50,000 pounds suspended fine.
Sione Faka'osilea is Romania's one ineligible player after previously representing Tonga Sevens. "That, however, is a very long way from saying that the Panel should overturn the result once it had been played and we have declined to do so".
"The committee's decision and findings clearly demonstrate issues with the processes adopted by some of the participating unions relating to the eligibility of players as well as the delivery and organisation of the Rugby Europe Championship".
World Rugby said it will oversee the appointments of all future match officials in Rugby World Cup qualifiers. Further, there is no precedent for a Disputes or Disciplinary Committee to set aside the result of a match in such circumstances.
"Rugby Europe deeply regrets this situation, " the body said in a statement.
Eligibility for global rugby is a notoriously complicated affair, with countries often nominating their own choice of "capture" level team that ensures a player can not then switch nationalities.