Last season's treble winners were held to a scoreless draw by Rio Ave - cup runners-up twice in 2013-14 - at the Estadio Municipal de Aveiro before goalkeeper Artur's shoot-out heroics.
Artur saved three spot-kicks to see Benfica win the Super Cup for the fifth time and first since 2005.
Both teams had their chances during the first 120 minutes – Jorge Jesus' Benfica arguably the better – without finding an opener.
And it would be left to Artur to be the hero.
The 33-year-old stopped the first shot of the shoot-out and the final two to lead Benfica to victory.
Yonathan Del Valle had his average penalty saved by Artur down low to his left, only for Benfica striker Derley to also be denied.
Filipe, Lima, Ukra and Bebe all scored to leave the shoot-out locked at 2-2.
Diego Lopes had his saved down to Artur's left before Luisao gave Benfica the advantage.
Tiago Pinto was the last player to be denied as his spot-kick was saved, ending Rio Ave's bid for a first Super Cup.
