Barca's own route to the final proved more problematic, as a heated 1-1 draw against Atletico Madrid at Camp Nou - which sealed a 3-2 aggregate success - came at the cost of red cards for Sergi Roberto and Suarez, though the latter is subject to appeal.
A video published on the website of Spanish daily Marca showed groups of supporters, some of whom were carrying metal bars, fighting outside a bar in the university area of the city of Vitoria, throwing chairs and tables.
Barcelona have 48 points after 22 games.
Both sides later released statements condemning the violence.
Samuel Marsden covers Barcelona for ESPN FC.
Alaves said they will consider necessary sanctions if their season-ticket holders are among those implicated. If yesterday's match at Mendizorrotza is anything to go by, May's Copa del Rey could be a non-event.
And with the scoring completed before the 70th minute, Barca were able to take their foot off the gas in preparation for Tuesday's Champions League game against Paris Saint-Germain.
Messi went close after three minutes, while Vidal fired over shortly before Hernandez gave Barca a fright with a galloping run, which was only stopped by a fine stop from Ter Stegen.
"Nili is one of few B team players with first division experience, playing for Las Palmas, and I make the decisions".
Alaves - who had denied Barca a goal on the Catalan giants' last three LaLiga trips - had barely recovered from that blow when they conceded a poor second, goalkeeper Fernando Pacheco punching an attempted clearance into Suarez and the loose ball falling for Neymar to tap in.
The champions hit top form after the break with four more goals in eight minutes.
But the win was ultimately overshadowed by a frightful ankle injury to Vidal in the closing stages, the right-back colliding with Alaves youngster Theo Hernandez in a 50-50 tackle.
"The approximate downtime will be about five months".