Sevilla said they could file a complaint ahead of the game in Tangier, Morocco if Barca name an "improper lineup".
Ousmane Dembele scored a late winning goal with a blistering strike from outside the area.
But Ben Yedder hit a weak penalty in the Sevilla vs Barcelona gamenwhich was easily saved by Ter Stegen.
Sevilla then hit the crossbar from Franco Vazquez's looping header as both sides pushed for victory.
The video assistant referee (VAR) was used for the first time in Spanish soccer to award the goal, which had initially been ruled offside.
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.
A year ago, Barcelona broke their own transfer record to sign Dembele from Borussia Dortmund in August for a fee of 105 million euros (now $120 million) that could rise to 147 million euros.
Arturo Vidal came off the bench for his Barcelona debut late on, and there was drama in the final moments when Ter Stegen brought Aleix Vidal to the deck to hand Sevilla the chance to level from the spot. We've done it, ' Sevilla boss Pablo Machin said. "He is a very young player and we hope that little by little he makes progress".
Sevilla qualified for Sunday's match as last season's Copa del Rey runners-up, after Barcelona won the league and cup double.
This is also the first year that the trophy will be decided over one game, with the Super Cup previously a two-legged affair.
Sevilla FC is surprised by the RFEF's announcement 24 hours before the Super Cup. In their last notice for the 18-19 season, only three were due to be permitted, without exception.