Leonardo Jardim's side were already assured of second place and came into the last day of the season off the back of a 1-1 draw with Nacional.
But they were unable to sign off the campaign with a victory in front of their own fans - Evandro scoring the only goal of the match from a fifth-minute penalty.
The defeat is Sporting's first on home soil in any competition since February 2013, and sees them finish seven points adrift of champions Benfica.
Estoril were already guaranteed fourth position and will enter next season's UEFA Europa League at the play-off stage.
And Diogo Viana's penalty just after the half-hour mark ensured the strugglers' campaign enjoyed a happy ending.
In the day's remaining fixture, Derley scored a winner seven minutes from time to seal a 1-0 victory for Maritimo at home to Rio Ave.
