It was Barcelona's 13th Supercup and sixth in the last nine seasons.
Pablo Sarabia opened for Sevilla in the ninth, when the video assistant referee overruled an offside call in the first use of VAR in Spanish competition.More news: Ronaldo nets first Juventus goal in friendly against B team
Gerard Pique, who announced his worldwide retirement with Spain on Saturday, levelled three minutes before the interval for Barcelona after he was fastest to respond to a loose ball following a Messi free-kick.
Sevilla were then awarded a penalty in the 90th minute when Ter Stegen committed a foul in the box.
Barca, therefore, could easily field only three non-EU players rather than risking the match.
The federation's rules normally only allow for teams to register five non-EU and use three in a matchday squad for La Liga games, and Sevilla made their objections clear on Saturday night.More news: Arsenal vs Manchester City
It had been thought the Spanish Super Cup was the same but Sevilla said they would object to "an improper line-up".
Arturo Vidal, Malcom, Arthur and Marlon are Barcelona's four non-EU players who have travelled to Morocco.
Luis Suarez squandered a glorious chance for Barca after 28 minutes, with the Uruguayan heading over the crossbar from six-yards out after being picked out by Lionel Messi.
The Spanish Super Cup preceeds every La Liga opener and the match it is between La Liga champions against the Copa del Rey winners, but since Barcelona won the domestic double last season, Sevilla qualify as Copa del Rey runners-up.More news: Ben Chilwell: 'Harry Maguire will not leave in January'