The Spanish Rugby Federation (FER) apologized on its website, saying it "regrets the reaction of some players who did not contain their mood at the end of the match".
Questions following the final whistle centred on the appointment for the fixture of Romanian referee Vlad Iordachescu and two Romanian assistant referees, with Spain's players angrily confronting the referee at the final whistle and sarcastically applauding his performance, leading to Iordachescu being escorted from the field by security.
Spain's loss means that Romania qualifies for the 2019 World Cup as they finished second on 14 points at the expense of Spain who finished third with 13 points in the Rugby Europe Championship standings.
Spain were overwhelming favourites to beat Belgium but rarely got going on a mud-caked pitch in Brussels and ugly confrontations broke out at the final whistle as members of the Spanish coaching staff tried to restrain their players.
Here are some photos of the scenes after the game.
Spain must now beat Portugal in a playoff to maintain any hopes of reaching the 2019 tournament in Japan, with the victor facing Samoa in a two-legged tie.
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"The image at the end of the game does not represent the sport nor the values of this team".
Not helped by a poor pitch worsened by snow in Brussels the night before, Santos's side struggled in the first half and went into their dressing room at halftime trailing 12-0.
"When we were trying to come back in the game the play kept on being interrupted". Jaime Nava, the Spain captain, said that his side had been "eliminated by external factors", adding: "Today rugby has lost". "He gave 10 penalties against us, the result comes from that".
Romania will join Six Nations champions Ireland, Scotland, Japan and another playoff victor in Pool A. They were expected to have to endure the harder qualifying route after it lost to Spain 22-10 in Madrid last month for the first time in six years. Georgia automatically qualified for the Rugby World Cup at the 2015 tournament.
Romania has played at every Rugby World Cup but never advanced beyond the pool stage, AP reported.