Torres, who made his debut at Atletico's atmospheric home of 51 years aged 17 in 2001, knocked in Antoine Griezmann's glanced header from close range in the eighth minute then swivelled to hook a bouncing header from Koke into the net in the 11th.
Substitute Inaki Williams gave Athletic hope of a comeback midway through the second half to boost their chances of finishing sixth but Angel Correa struck the final goal in the league at the Calderon in the 89th minute.
The stadium hosts the King's Cup final between Barcelona and Alaves next Saturday, while a friendly between Atletico and a "Legends" side composed of former players from the club next Sunday will be the final game there, with Atletico moving to the 67,000 capacity Wanda Metropolitano stadium next season.
Atletico finished third with 78 points while Athletic missed out on sixth and a qualifying round spot in next season's Europa League to Basque rivals Real Sociedad, who snatched a 2-2 draw at Celta Vigo with an added time leveller from striker Juanmi.
Athletic are seventh but can still earn a place in the Europa League if Barcelona win the King's Cup.
Later on Sunday, Real Madrid will clinch their first league title since 2012 by avoiding defeat at Malaga, while Barcelona host Eibar needing a win and a victory by Malaga to lift a third consecutive domestic crown.
(Reporting by Richard Martin; Editing by Ken Ferris)
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