The Catalans had to come from behind twice before sealing victory, with Neymar, Rafinha and Messi all finding the back of the net to cancel out goals from Denis Cheryshev and Luciano Vietto.
The Argentine has often been deployed as a deep lying playmaker in Luis Enrique's new-look system, but operated as a winger on Sunday - a move the coach defended after the game.
He said: "Messi playing on wing again? It's for the good of the team, but he has freedom to move. We want him to touch the ball a lot."
Luis Suarez again toiled away up front for Barca but failed to convert several chances that came his way, meaning he has just five goals in 18 games in all competitions for the club this season.
But Luis Enrique again offered his backing to the Uruguayan, insisting his contribution was more than just about scoring goals.
"What does Suarez add? A lot," he continued. "It's crucial to have someone to push back the centre backs. The goals will come, no doubt."
The Spaniard also reserved special praise for Rafinha, who scored his first goal for the club, and Andres Iniesta, who shone in a central role.
"Rafinha? He had a very complete game, like the others. This season, he needs to adapt a bit. No doubt he'll be a key player for Barca.
He added: "Iniesta is playing at best position now, more in centre, not as much from wing as before. I'm very happy with performances."
The result leaves Barcelona one point behind leaders Real Madrid at the top of La Liga, but Carlo Ancelotti's side have a game in hand.
