League leaders Barca tried to have the game postponed, but their request was turned down by La Liga and the club announced 25 minutes before kickoff that the game would be played behind closed doors.
Barca's Sergio Busquets scored for the first time in the league in three seasons to give the hosts the lead in the 49th minute, leaping to head in a curling corner from Messi.
Argentine Messi then struck his 10th league goal of the season to double Barca's advantage in the 70th.
He barely celebrated the strike, adding to an atmosphere more akin to a training ground exercise than a league game.
Messi then latched onto a pass from fellow forward Luis Suarez to pounce again in the 77th, sealing Barca's seventh straight win of the league season and maintaining their 100 percent start in La Liga and the Champions League.
Barcelona lead the standings on 21 points, five clear of Sevilla in second. Champions Real Madrid, who are sixth on 11 points, play at home to Espanyol later on Sunday searching for a first home win of the season in the league.
Bizarre circumstances
The bizarre circumstances of the game appeared to affect Barca in the first half as they lacked energy and imagination, mustering only two shots on goal -- an early strike from Sergi Roberto and a wayward header from Paulinho.
Las Palmas, who stoked tensions by wearing a Spanish flag on their jersey for the game, came closest to scoring just before the interval when Argentine Jonathan Calleri struck the post.
The home side looked far more composed as a result and were eventually worthy winners.
"It was very strange, of course it’s not normal but today’s events overshadowed the game," Busquets said on playing behind closed doors.
"Today was a special day, we had to focus on the sporting part, which wasn’t very nice for us, and we were affected by everything as other things were on our minds," he added.
"We struggled a lot in many senses and the first half performance was very bad. We were better in the second, we dominated in every aspect and are very happy with this run of victories."