Barcelona needed spot-kicks to see off Betis after an entertaining draw over 120 minutes at Riyadh’s King Fahd Stadium.
Robert Lewandowski put Barcelona ahead after 40 minutes but Betis playmaker Nabil Fekir levelled with 13 minutes remaining.
Ansu Fati smashed in a fine volley to put Barcelona ahead in extra-time but Loren Moron pulled Betis back level with a cunning backheel flick.
Ter Stegen denied Juanmi and William Carvalho in the shootout and Pedri converted the decisive spot-kick.
Barcelona have not won the Spanish Super Cup since the change to a four-team format, with the first Saudi Arabia edition taking place in 2020.
After finishing last season without a single trophy and investing heavily in the summer despite the club’s debts, Xavi and his team are desperate for silverware, with Sunday their first opportunity to get their hands on some.
Pedri had an early strike disallowed for offside as the Catalans started well, but Betis soon found their comfort zone, inspired by the artistry of Fekir and dynamism of Luiz Henrique.
However, Lewandowski, who missed the win over Atletico Madrid in La Liga on Sunday through suspension and was far from his best, broke the deadlock shortly before the break.
The Polish forward’s first effort was blocked but he brought the ball under his control again and managed to beat Claudio Bravo at the near post.
Ter Stegen made saves from Rodri and Henrique to keep Barcelona ahead, on a busy night for the German goalkeeper.
Fekir eventually levelled in the 77th minute after clever footwork from Henrique, who set him up, and the French midfielder drilled past Ter Stegen at his near post to force extra-time.
Three minutes into the additional period, Fati produced a piece of magic to put Barcelona back in front with a volley from the edge of the box.
It didn’t last long, with Betis striking through Moron’s clever effort, backheeled past Ter Stegen despite close attention from Ronald Araujo.
Fati tried to reply with a backheel of his own but former Barcelona stopper Bravo was alert to deny him.
Veteran Betis midfielder Andres Guardardo was sent off late in extra-time for two yellow cards, but Barcelona did not have long enough to capitalise before penalties.
Both sides converted their first two spot-kicks but Ter Stegen denied Juanmi to hand the Catalans the advantage.
Fati scored and Ter Stegen produced another save to foil Carvalho, with Pedri converting the next spot-kick to seal Barcelona’s progress.