Benfica president Luis Felipe Vieira has described his team's Champions League exit to Chelsea as "an outrage" and vowed to protest to the Portuguese Football Federation.
Chelsea, having won the first leg of the teams' quarter-final 1-0 in Lisbon, booked a semi-final date with Barcelona after securing a 2-1 victory at Stamford Bridge, but the return leg was not as straightforward as had been expected.
Benfica, who played most of the match with ten men after Maxi Pereira was shown a second yellow card in the 40th minute, were within a goal of progress following a Javi Garcia header in the 85th minute only for Raul Meireles to settle the encounter in the dying moments.
It was an impressive showing for a team many had written off after the first leg, and there was a feeling in the Benfica camp that referee Damir Skomina had unduly influenced the tie.
"Whether we were there (in Lisbon) or here (in London), we were not allowed to eliminate Chelsea," Vieira told RTP. "Benfica were the better team and deserved to go through, but other factors seriously hindered us. We lacked luck."
Vieira, who added that "only the officials failed to see" a John Terry handball in the area in the first leg, suggested the fact that Portuguese football is "very small" meant the authorities showed a preference for teams from the bigger leagues.
"We can't understand how a Slovenian referee was in charge of this match and we will explain our position to the Portuguese Football Federation," he said. "I don't know whether the federation is capable of doing anything.
"Surely everyone saw what happened here. It is evident that this is a business and that there was no desire to see Benfica go through. Refereeing has reached a scandalous point."
Benfica manager Jorge Jesus similarly felt that Skomina, who issued eight yellow cards in the second leg, had played a part in his team's demise.
"Well, we've been the better team in both legs - in Lisbon and in London,'' he said. "I am very proud of my men. We played with ten men for the best part of an hour and we were still the better team. We made Chelsea look ordinary.
"We were penalised by the referee tonight, unfortunately, and unjustly I feel, but that's football in the end. We come away as losers but I feel my team gave everything and I am very proud of my players tonight."
He added: "Over the two games we proved we were much the better team. What hurts me is that we've knocked out better teams than this Chelsea. I may be wrong but I believe Chelsea have no chance against Barcelona."
Despite their disappointment, Vieira remains confident Benfica will return to the Champions League next season ready to try again. "We'll be back," he said. "UEFA and Platini will see Benfica again in Europe."