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After a difficult start to his time at Atletico, Felix now has six goals in his last six LaLiga appearances.
"It's a natural process for players, some players arrive and play, others begin on the bench, it depends on the player," Felix said afterward. "I never stopped working, I always tried to do my best, and when you do that the truth rises up. The team is doing well."
Added Simeone: "He keeps growing, he's in great form. He's happy, he's well, he's working hard and he's doing everything that we need of him."
Felix opened the scoring in the 10th minute with a close-range header from a Sime Vrsaljko cross.
However, Atletico lost focus and allowed Alaves to score the equaliser with a Gonzalo Escalante header in the 63rd minute.
After Brazilian striker Matheus Cunha was fouled inside the area, Suarez scored from the spot to put Atletico back in front.
With Felix extending their lead in the 82nd minute, an on-fire Cunha, who was making his comeback after being out for several weeks with an injury, produced a brilliant through pass to Suarez. The Uruguayan finished the match in style to complete an emphatic win for Atletico.
"The team keeps improving and growing," Simeone said. "Today was up and down, we started well, then we disconnected a bit. In the second half we didn't start well, we conceded the goal but had time to react. The team reacted well, with the changes, Suarez and Cunha came on and did well, Joao did well on the left. It's a game that's good for us to continue on the path we're on."
Alaves remained on 22 points, five points from the safety zone.
Atletico next travel to face Manchester City in their Champions League quarterfinal first leg on Tuesday.
"Now we'll rest, we need to rest from this effort. A lot of players have been with their countries, others back from injury and from tomorrow we'll think about the opponent we have," Simeone added.
ESPN's Alex Kirkland contributed to this report.