Málaga's Champions League journey ended in the cruellest way with two stoppage time goals from Borussia Dortmund on Tuesday, the second of them apparently offside, snatching a semi-final place from their grasp and leaving players, manager and owner pointing an accusing finger at Uefa.

Suspicions over the way that they were knocked out were expressed in the aftermath of a barely believable end to the quarter-final.

The club's director general, Vicente Casado, said before flying home with the squad that Málaga would file a written complaint to Uefa about decisions made by the Scottish referee, Craig Thomson, and his team while the club's Qatari owner, Sheikh Abdullah al-Thani, said on Twitter: "I'm sorry to go out this way [to] injustice and racism."

There was no consolation for a side that have performed superbly in their first appearance in the competition, their achievement temporarily lost in the swirl of suspicion. "Football owes you one, Málaga," ran a headline. The response from many was obvious: Uefa does.

"The pride will come later on but for now the dressing room feels frustration. There are ways of going out and going out like this hurts more," the defender Martín Demichelis said. José Ramón de la Morena, the presenter of the Spanish radio show El Larguero, asked Joaquin what he could do to cheer him up. The attacker replied: "Nothing."

There was stunned emotion in his voice as Joaquin added: "Of course we suspect Platini and all of those [in Uefa] because we're not Real Madrid, we're Málaga and it is much easier to do this to us."

For Al-Thani there was a different explanation. "This is racism… I hope to open a thorough investigation Uefa regarding the Spanish club out this way. Which does not effect the spirit of sport," he tweeted, overlooking the fact that Uefa's president backed Qatar's bid to host the 2022 World Cup.

He later tweeted: "Yes, we were targeted from the beginning of the season by corrupt Uefa and based on racism."

The Uefa general secretary, Gianni Infantino, responded by promising the comments would be assessed by the governing body's "disciplinary inspectors". He added: "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."

Al-Thani's view was not echoed by anyone else at a club where players have gone unpaid and there have been numerous remarks underlining the fact that players and staff consider Málaga's success theirs, not his. But they had their own doubts.

As the clock ticked beyond 90 minutes, Málaga were 2-1 up and Dortmund needed two goals. The first came after 91 minutes, then, in the 93rd, Santana nudged over the line to complete the turn round.

At the final whistle Málaga's players slumped to the turf. When they got up again, they made their way to the dressing room to see the final goal replayed and have their suspicions confirmed. There were in fact two offsides: when the ball was curled into the area, four men were in an offside position and, when it finally dropped to Santana on the line, he too was offside.

Málaga had previously been banned from Uefa competitions for next season because of outstanding payments owed but the club have appealed and will take the case to the Court of Arbitration for Sport in the summer.

Although Málaga's second goal was also offside and Dortmund had an earlier "goal" correctly disallowed for offside, Málaga's manager, Manuel Pellegrini, said the result was not coincidental.

"It was difficult for a banned team to reach the semi-finals," he said. "There is not one offside, there are two of them and that is not an isolated occurrence. They damaged our chances in the last 10 minutes of the game. They pushed us into our area with shoves and elbows.

"At 2-1 there were even a couple of red cards that were not given. What happened is something that's beyond our control. It is very hard to swallow a defeat when it happens like this. It's bitter."

Roque Santa Cruz also expressed his disappointment after the defeat. "We all made a super-human effort and going out of the competition because of a mistake like that is painful," the forward told Spanish television. "We were four minutes away from the semi-finals and it was snatched away from us. Now we have to lift our spirits and tackle the rest of the season in the best possible way."

"This can't happen because it just can't," said Joaquin. "Shit, they throw all your hard work on the floor. You run and fight and you can't imagine anything like this happening. The manager said that a team that is banned by Uefa could not go through and that's completely true. We have to say so because today it is us but next time it might be someone else. We don't deserve this. Nobody does."