Barcelona's La Liga game against Las Palmas was played behind closed doors as a protest after their request for it to be postponed in light of Catalonia's independence referendum was rejected.
The Spanish government pledged to stop a poll declared illegal on a day of violent protests and unrest.
Barca took the decision to play behind closed doors 25 minutes before kick-off, with thousands of fans outside, reports BBC.
“This (playing without fans) was a measure to show our rejection of what took place today,” Bartomeu told television network BeIn Sports.
The league leaders, however, cruised to a comfortable 3-0 victory.
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 domestic league win this 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, while Real are fifth on 14. Valencia, with 15, climbed above Atletico Madrid on goal difference, according to Reuters.
Catalonia, a region of 7.5 million people in north-eastern Spain, has its own language and culture and Barcelona is its capital.
It also has a high degree of autonomy, but is not recognised as a separate nation under the Spanish constitution.