Captaining a second-string Atleti side – playing four days on from their Europa League triumph against Marseille in Lyon – at a celebratory Wanda Metropolitano, Torres netted either side of the interval in Sunday's clash.
Having cancelled out Kike Garcia's opener just before the break, Torres edged Atleti ahead on the hour, rolling back the years with a fantastic run and delicate finish.
Any hopes Torres had of making way to a standing ovation were ended shortly after he netted his second, though, as Jose Gimenez entered the fray for Atleti's third change after Lucas Hernandez had seen red.
And Eibar were quick to make their numerical advantage count, Pena hammering in a thunderous long-range strike to haul the visitors level with 20 minutes remaining.
Antoine Griezmann could well be leaving Atleti during the off-season, and he looked set to mark his would-be final appearance with an assist late on when he teed up Torres, but his hat-trick goal was denied by the offside flag as Simeone's men settled for a share of the spoils in their final LaLiga game of the campaign.
Torres should have got his farewell game off to a great start inside 10 minutes, but the veteran dragged his effort wide after getting in behind Eibar's line in trademark fashion.
Saul Niguez was the next to go close as Atleti upped the pressure - the Spain midfielder curling wide from the edge of the area.
Desperate to set Torres up, Filipe Luis did brilliantly to get down the left and pick out the striker, who was unable to turn home at the near post, and Atleti would soon be made to pay for that miss.
Jan Oblak's hesitation allowed Kike to latch onto Joan Jordan's throughball, the former Middlesbrough forward making no mistake with a cute first-time finish into the bottom-right corner.
Eibar's lead would be short-lived, though, as Atleti's man of the moment stepped up.
Angel Correa beat Eibar's offside trap and, having drawn Marko Dmitrovic off his line, squared coolly to Torres, who duly slotted into an unguarded goal.
Simeone responded to a sluggish start to the second half in aggressive style, introducing Griezmann and Diego Costa from the bench as Atleti hunted a second.
Those changes swiftly paid dividends, Costa threading a pass into Torres, who burst clear of his marker before lifting a neat effort over the onrushing Dmitrovic.
Hernandez could have conceded a penalty for handball early in the second half, but his luck ran out when Atleti were reduced to 10 men in the 63rd minute - the France youngster receiving his second booking for a clumsy tackle on Ivan Alejo.
Eibar wasted little time in restoring parity, Pena lashing a venomous half-volley into the top-right corner.
Griezmann proved his quality with a sublime touch and pass into Torres in the closing stages, but the linesman's flag dashed the former Liverpool forward's hopes of bringing the curtain down on his Atleti career with a hat-trick.
That did not detract from Torres' farewell celebrations, though, as he received a guard of honour from his team-mates and the Atleti coaching staff after the final whistle.
Key Opta stats:
- With his first goal, Fernando Torres scored his 128th goal for Atletico in all competitions, 6195 days after his first one against Albacete in June 2001 in the Segunda Division.
- Torres has finished his Atletico career as the club's fifth all-time top-scorer with 129 goals, five fewer than the fourth (Jose Eulogio Garate, 134).
- Against Eibar, Fernando Torres has scored his 100th for Atletico in all competitions (6th February 2016) and his last one (a brace today).
- Torres is the only Atletico player to have scored two braces at Wanda Metropolitano this season in all competitions.
- Atletico have conceded four goals in their last two La Liga games at Wanda Metropolitano, as many as they had in their previous 17 (four).
- Lucas Hernandez has been sent off for the first time in his Atletico career (88 games in all competitions).