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.
"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 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.
However, Pacheco sprang 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 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.
Elsewhere, Koke scored a sensational double as Atletico Madrid made light of Antoine Griezmann's absence through suspension to register their first win of the campaign with a 5-1 rout of Las Palmas.
Angel Correa and Yannick Carrasco got the visitors off to the perfect start in the Canary Islands inside five minutes.
Jonathan Calleri briefly gave Las Palmas hope with a towering header after the break, but Atletico instantly replied when Koke curled into the top corner from 25 yards.
Girona got their first ever win in the top flight as Pedro Alcala scored the only goal in a 1-0 win over Malaga.
Levante fought back from 2-0 down to rescue a 2-2 draw at home to Deportivo la Coruna thanks to Ivi's late penalty.
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