The Madrid-based side has registered just 21 players for the current season instead of a possible 25. To further exacerbate their situation, they lost club captain Antonio Lopez to injury recently.
At the Mestalla, they faced a Valencia squad determined to put in a good showing after their recent poor form that has seen them struggle to hold onto the third-place position in La Liga.
But Atletico were determined to reach the final for the second time in three seasons. They last won the Europa League in 2010 when they beat Fulham in the final and with their one-goal win over the Valencians, they have a chance to win a continental trophy unlike their cross-town rivals Real Madrid who lost out to Bayern Munich on Wednesday night.
"I am very happy, mainly for the players, who have made an enormous effort. What they do is heroic," announced Simeone in a press conference after the win.
"Playing on Sunday, on Thursday and then on Sunday again for almost two months with a small squad. We also had some injuries to important players such as Antonio López and Silvio, who have barely been able to help us.
"Obviously, I am delighted for all the Atlético fans because today [Thursday] they are proud to support this team."
Now the Rojiblancos get to face Athletic Bilbao in the final in Bucharest on May 9. Bilbao, led by Marcelo Bielsa, have conquered Manchester United, Schalke and Paris Saint-Germain in the run-up to the final. However, they lost to Atleti in La Liga in their most recent encounter on March 21.
"Athletic are having a superb tournament. They are going to play in the final of the Copa del Rey and will now also play in the Europa League final. I can only congratulate them," commented Simeone.
"It will be a nice final between friends but we want to win. I am very proud to be back at Atlético and I feel a lot of responsibility.
"Today, Atletico fans will go to bed very happy."
Atletico can still qualify for the Champions League through the league as they are four points behind fourth-placed Malaga with just four games remaining. They visit struggling Real Betis away in their weekend league fixture on Sunday.