MORE: Muller comes up bloody | Bad actor | Match images | Messi beaucoup | Bradley needed
The Juventus man started France’s opening game against the Central Americans, where, despite impressing with his performance, he was criticized for a spat with Wilson Palacios.
The Honduras midfielder appeared to trample on Pogba, leading to the French midfielder kicking out in frustration, for which he was fortunate only to receive a yellow card.
Pogba was used only as a second-half substitute in the 5-2 thrashing of Switzerland in France's second group game, but Deschamps insists it was a tactical decision to deploy Moussa Sissoko instead.
"That was not a sanction against the fact that he could have received a red card in the first game," he said. "It was a choice with respect to Moussa Sissoko.
"Paul has huge potential, I trust him, and he knows that. He is capable of doing very good things. But I cannot play all players."
Deschamps and France sealed qualification for the last 16 with their win in Salvador and will play Ecuador on June 25 at the Maracana in their last group game.