In a tight opening, Barcelona opened the scoring after 25 minutes courtesy of Messi, who headed home an Alexis Sanchez cross.
Messi might have doubled the lead moments later, but he fired wide from close range before Sanchez and Andres Iniesta also tried their hand.
Mallorca were struggling to influence proceedings in the first period, and the second half started much the same with Messi coming close after 55 minutes.
Barcelona lost Thiago to a red card early in the second period, but it did not stop their dominance.
The home side did come close via a Tomer Hemed header after 57 minutes, before Hemed again tested Victor Valdes with 20 minutes remaining.
Barcelona all but secured the win, however, after 79 minutes when Gerard Pique struck from inside the box to send the Catalans 2-0 ahead.