The Blaugrana showed faith with the first line-up from the 1-1 draw against Paris Saint-Germain in the UEFA Champions League last 16 second-leg.
Barcelona grabbed the lead in the 13th minute with a stunning left-footed finish from Messi after he met a ball from Sergio Busquets.
Messi went close to a brace two minutes later from a cutback inside the six-yard area, but the Argentine saw the attempt fly over the top of Alvaro Llorente's goal with the defence unstable.
A lovely bit of play from Huesca before the half-hour mark presented Pablo Maffeo an opening, but goalkeeper Marc-Andre Ter Stegen came out to parry.
Barcelona bagged the second goal ten minutes before halftime after Antoine Griezmann beat one challenge to cut in outside the area before finding the top-corner.
A third goal almost arrived minutes to the break through a tap-in from Frenkie De Jong following a loose ball in the area, but the crossbar rescued the visitors.
Huesca received a glimmer of hope on the cusp of halftime when Rafa Mir fired in from the penalty spot following a foul by Ter Stegen.
The Catalan giants restored their two-goal advantage six minutes from the break with a thumping header in a crowded area by Oscar Mingueza following a cross from Messi.
Mir closed in on a brace inside the final quarter from a cutback in the area by Dani Escriche, but the former couldn't capitalise.
Barcelona looked to contain matters inside the last 20 minutes, as Griezmann made way for Francisco Trincao and Ilaix Moriba introduced for Sergio Dest.
After a quiet spell, Huesca conceded a fourth in the dying minutes after Messi curled into the bottom-corner from outside the area to see out the clash.
