Thanks to an extra-time screamer from Inaki Williams, Barcelona head coach Ronald Koeman was left empty-handed in his search for his first silverware as boss of the Blaugrana.
They would eventually lose 3-2 in the final, and to make matters worse, Messi's frustration got the better of him as he lashed out at Asier Villalibre with a slap to the back of the head.
He was subsequently dismissed for the first time in his Barcelona career and handed a two-match suspension.
It is, however, unlikely that Messi would have played from the start in the Copa del Rey, with the Blaugrana taking on a Spanish Segunda B side.
There could also be other rotation as Koeman looks to keep his key players fresh for La Liga action versus Elche on Sunday.
Marc-Andre ter Stegen will probably make way for Neto, with Samuel Umtiti possibly given a start in the middle of the defence with Clement Lenglet dropping to the bench for a rest.
Oscar Mingueza, too, might come in for a new central defensive partnership from the weekend, replacing Ronald Araujo.
With Sergi Roberto still injured, Sergino Dest will have to continue at right-back, but Junior Firpo might replace Jordi Alba at left-back.
Dest was replaced at half-time against Athletic but is thought to be fine to start in the cup. If not, Mingueza could play at right-back instead.
Miralem Pjanic is certain to start, probably at the expense of Sergio Busquets.
Pedri might move into a more advanced role, with Francisco Trincao replacing Ousmane Dembele on the right of the three behind the striker, with Martin Braithwaite coming in for the suspended Messi.