Mikel Arteta’s side secured a place in their first Champions League final in 20-years with a 2-1 aggregate win over the Spanish side.
Arsenal could be considered a little lucky, however, with Atletico having two penalty shouts due to incidents involving Riccardo Calafiori.
Speaking in a sensational rant on Wednesday, Martinez-Almeida said: “Well look, what I'm saying is that when I saw the draw I thought we'd get Arsenal and I was wrong.
“We got to play against UEFA. And UEFA has made it clear that they didn't want Atletico Madrid in the Champions League final.
“It's incomprehensible that they appointed a German referee when Spain and Germany are playing for the fifth Champions League spot.”
The first incident saw Giuliano Simeone go down under a challenge from Calafiori, but the Atletico man was deemed to be offside.
Reacting to the decision, Martinez-Almeida said: “It's incomprehensible that there isn't a single replay of Giuliano's offside when it was a clear penalty.
“We later saw on social media that it wasn't offside and that he left his own half. In a match broadcast by so many television cameras, why didn't the production team show a replay to determine whether it was offside or not?
“Because it wasn't offside, and they refused to admit it.”
A second penalty shout involving Calafiori and Antoine Griezmann was also dismissed, and again, Martinez-Almeida didn’t take it well.
“There's intent in my opinion. I insist, Arsenal could have been beaten, but we couldn't beat the UEFA Cup and it was impossible to beat it," he said.
“We drew the UEFA Cup, not Arsenal, in the draw to go to Budapest. That's why I think we Atletico fans are proud of our team because they competed not against Arsenal, but against UEFA.
“You can beat Arsenal over 180 minutes, but you can't beat UEFA. And UEFA set in motion the entire machinery to prevent Atletico Madrid from advancing in yesterday's match, and the referee was the one who carried out that will.”