Abdullah Bin Nasser Al-Thani's claims were dismissed by UEFA on Wednesday, moments after the governing body of European football disclosed proposals for new sanctions against racism.
Al-Thani's outburst came after Malaga missed out on a spot in the Champions League semifinals. Borussia Dortmund scored an injury-time winner Tuesday from what looked to be an offside position.
"We were targeted from the beginning of the season by corrupt UEFA and based on racism," Al-Thani wrote Wednesday on Twitter, adding to the criticism posted online immediately after the 3-2 loss.
UEFA general secretary Gianni Infantino said Al-Thani's tweets will be looked at.
"It will now be analyzed by our disciplinary inspectors," Infantino said at the SoccerEx conference. "I can understand when you lose a match in the 93rd minute the emotions come up and maybe you say things that you don't really think and you really don't want to say."
Malaga was already angry with UEFA after being banned from European club competitions for next season for failing to pay player wages and tax bills on time.
"I don't know in which sense there would have been racist abuse (behind UEFA's decisions)," Infantino said.
In the build-up to Felipe Santana's winner for Dortmund, teammates who touched the ball appeared to be offside.
Malaga director general Vicente Casado said the Spanish club will be making an official complaint to UEFA over the refereeing, but Craig Thomson and his team of officials was defended by Infantino.
"The referees are always in good faith," Infantino said. "They are doing very difficult job ... they can make mistakes like anybody."
Al-Thani's allegations took the focus off UEFA's announcement of beefed-up sanctions for racism.
"The fight against racism is something that is very serious and we have to always have zero tolerance," Infantino said. "We have to make sure there is concrete action, not only words."
The UEFA executive committee will next month be asked to give final approval for punishments, including a minimum 10-match ban for players or officials found guilty of abuse.
While UEFA can only enforce the punishments in its competitions, UEFA's 53 members will be asked at next month's congress to adopt the same measures.
"We just felt it's time to send out a strong message," Infantino said.
UEFA wants to double the current minimum ban of five matches that players and officials currently face for racial abuse.
In England in recent years, Liverpool striker Luis Suarez received an eight-match ban for racially abusing an opponent and Chelsea captain John Terry was suspended for four matches.
"We have to have sanctions and they must have a deterrent effect," Infantino said.
The debate on racism in European football intensified this season after AC Milan midfielder Kevin-Prince Boateng's decision to lead his team off the field during a friendly in Italy after facing abuse.
UEFA has been criticized in the past for only fining national associations for racist abuse by fans.
Under the new plans, the first sanction for clubs will be a partial stadium closure — the stand where the abuse emanated from. If there is further racism in the stands, Infantino said there will be a "full closure of the stadium and a minimum fine of 50,000 euros ($65,500)."
On Wednesday, UEFA ordered Dynamo Kyiv to play a European club competition match next season in an empty stadium because of racist conduct by its supporters during home matches in the Champions League and Europa League.
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