Neymar opened the scoring with a simple finish from Messi's through ball before the Argentine star missed from the spot for the 12th time in his career after Loukas Vyntra had seen red for tripping him inside the area yesterday.
However, it mattered little as Ivan Rakitic's fierce strike made it 2-0 before half-time and goals from Sandro Ramirez, Pedro Rodriguez and Messi rounded off the scoring after the break to make it four wins in four La Liga games without conceding a goal for Barca.
"Once we have played a more significant amount of games we will look at the table and analyse our situation," said Barca boss Luis Enrique.
"But the season has just started and there will be a lot of changes in the table to come."
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Enrique recalled many of his rested stars for Wednesday's 1-0 win over APOEL Nicosia in the Champions League as he made eight changes in all with only Messi, Neymar and Dani Alves retaining their places in the side.
Barca then slowly began to take charge and after Jordi Alba fired wastefully off target, Neymar was denied at the end of a flowing move by a brave block from Jesus Fernandez.
The Brazilian got the better of Fernandez just after the half hour mark, though, as he latched onto Messi's ball over the top and rounded the 'keeper before slotting home his third goal of the season.