Without new signing Ousmane Dembele, who completed the second most expensive transfer ever by moving for 105 million euros ($125 million) from Borussia Dortmund on Friday, or the injured Luis Suarez, Messi ensured Barca didn't lose any early ground in the title race despite a tumultuous start to the campaign off the field.
The five-time World Player of the Year missed from the penalty spot for the 20th time in his career as Fernando Pacheco produced a stunning save midway through the first half.
However, Messi wasn't to be denied as his deflected effort opened the scoring shortly after half-time before a sweetly-struck volley secured all three points.
"We're happy because we have overcome a difficult test," said Barca coach Ernesto Valverde.
"We've overcome difficult moments, we have six points and we can now move forward."
Barca's pre-season preparations were rocked by the loss of Neymar to Paris Saint-Germain for a world-record 222 million euros.
Dembele has been bought to replace the Brazilian, but Barca's business may not be finished with a final push for Liverpool's Philippe Coutinho expected before the Spanish transfer window closes on Friday.
"We hope that by the 31st (of August) we have an even more competitive team, that is clear," added Valverde.
"We want an even better team and if there is a possibility we are open to it."
Messi magic
Alaves shocked Barca a year ago by winning at the Camp Nou, and the hosts were left to rue a big chance missed by Ruben Sobrino at 0-0 before succumbing to Messi's magic.
Sobrino burst past the leaden-footed Gerard Pique on the half-hour mark, but placed his shot too close to Barca 'keeper Marc-Andre ter Stegen as he bore down on goal.
Pique was involved at the other end as Barca were awarded a penalty moments later when he was hauled to the ground by Rodrigo Ely from a Messi free-kick.
Messi's record from the spot had improved greatly since he briefly quit international football after blasting a spot-kick over as Argentina lost the Copa America Centenario final to Chile little over a year ago.
However, Pacheco sprung to his right impressively to turn Messi's effort round the post.
Visibly annoyed at himself, Messi responded with the opening goal 11 minutes after the break as his powerful low drive struck helpless Alaves defender Alexis to fly past Pacheco.
Alexis was also at fault when Barca doubled their advantage 11 minutes later as his poor clearance was headed by substitute Paco Alcacer into Messi's path to smash home on his favoured left foot.
Messi could even have had a hat-trick as he saw another effort from the edge of the box hit the bar.
Yet Barca were never threatened after the break by an Alaves side lacking in ambition and attacking prowess as the hosts comfortably saw out a second 2-0 win to begin their league season.
And there was even the chance for Brazilian international Paulinho to make his Barca bow as he replaced Andres Iniesta for the final two minutes.