The 34-year-old, who has made more than 400 appearances for the club over two spells, netted either side of half time as Diego Simeone's team ended the campaign with a draw, despite being forced to play the majority of the final half-hour with 10 men.
Kike had earlier put Eibar in front before Torres turned the game on its head, but a second yellow card for Lucas Hernandez in the 63rd minute left Atletico with a numerical disadvantage for much of the second half.
Ruben Pena levelled things up again with 20 minutes remaining, but the hosts held out for a draw at the Wanda Metropolitano to finish the season in second place with 79 points - three clear of city rivals Real Madrid.
Torres was a threat throughout for the home side and had his first sight of goal after only 10 minutes when he collected the ball inside the area, only to fire well wide of the target.
The boyhood Atletico fan was closer to giving himself the perfect end to his illustrious career at the club shortly after the half-hour mark when he collected Filipe Luis's pass inside the box, but once again he could not find the target with the resulting effort.
Those misses looked as though they might prove costly when Eibar took the lead just three minutes later, with Kike doing well to bring Joan Jordan's pass under his spell before firing his finish into the bottom corner.
However, Torres restored parity three minutes before half time, and this time the former Liverpool and Chelsea forward could not miss as he tapped Angel Correa's cross into an empty net from close range.
A second followed for the Spaniard on the hour mark when he latched on to Diego Costa's pass to find himself one on one with the keeper, making no mistake with his finish.
Atletico's elation turned to despair just three minutes later when they were reduced to 10 men, with Lucas being given his marching orders for a second bookable offence.
It took only seven minutes for Eibar to make their numerical advantage count as Pena collected a loose ball on the edge of the area before firing his effort into the top corner to leave Atletico with 20 minutes to hang on.
Kike did almost inflict a second consecutive home league defeat on Simeone's side - something which has not happened since May 2013 - when he danced away from two defenders only to shoot narrowly wide from the edge of the box.
However, Atletico held out for the point just four days after winning the Europa League final against Marseille, while a point is also enough to guarantee Eibar a top-half finish.
ATLETICO MADRID (4-2-2): Oblak; Juanfran, Savic, Lucas, Kasmirski; Correa (Costa 59'), Gabi, Saul Niguez, Vitolo (Gimenez 66'); Koke (Griezmann 59'), Torres
EIBAR (4-2-3-1): Dmitrovic; Pena, Angel, Lomban (Arbilla 66'), Angel; Escalante, Garcia, Ivi (Charles 78'), Jordan, Orellana; Kike (Regis 93')