The Argentine star was unhappy with being replaced on Tuesday, but the Camp Nou boss has defended the decision as long-term thinking.
The Argentine star displayed discontent after being replaced in the second half of the Liga win, but the head coach insists that his decision was made in the best interest of the player and the club in the long term, while praising the team's overall performance.
"Messi never wants to be subbed off, but it's my task to take care of him," Martino told reporters after the match. "We need him at end of season as well as now. My way of thinking won't change, I repeated the whole time how I want to play, maybe this game helps some to see things clearer.
"We've played a very good game. The way we played in the first half was wonderful - it was a pity we couldn’t score more."
Martino went on to laud summer signing Neymar following his debut Liga goal, while insisting that Alexis Sanchez also played well despite not scoring.
"Neymar is an exceptional player," Martino said. "It has surprised us how hard he wants to work for the team.
"Alexis didn't score, but he worked very hard today, both in defense and attack. He does things that few forwards do."