Angel Correa and Antoine Griezmann put Atletico ahead before substitute Torres scored in his first match since announcing that he would leave his boyhood club at the end of the season.
Torres eventually sealed the win for Atletico in the 77th minute by turning home Correa's in the box.
However, in drawing Atletico in the semi-finals, Arsenal missed out on slightly easier ties against Marseille and Red Bull Salzburg.
The result also guarantees Simeone's side a place in the Champions League for a sixth consecutive season. "We will try to get closer to them and if we can't get closer, we will congratulate them".
Atletico will visit Arsenal in the first leg of their Europa League semifinal on April 26.
The Gunners may have faltered in the Premier League this term, but they will still be confident of salvaging their season by winning the Europa League. But the visitors' resistance was broken in the 33rd minute when Vitolo weaved inside to the edge of the penalty area and slipped the ball left to Correa.
Cristiano Ronaldo and Gareth Bale were both rested and Real Madrid hardly broke sweat as they beat Malaga 2-1 on Sunday to climb to third in La Liga.
Griezmann wasted a one-on-one situation with Oier Olazabal shortly before halftime when he was booked for diving after contact with the goalkeeper.
That was his last significant contribution, before making way for Torres just before the hour, and Koke was also spared the last 30 minutes, replaced by Gabriel Fernandez.