A deflected Ever Banega strike on 54 minutes and a curling free-kick from debutant Federico Mancuello three minutes from time secured a straightforward win for the World Cup finalists yesterday as they build towards June's Copa America in Chile.
Although Argentina football officials said early this week that tests showed Messi suffered no serious injury to his right foot when he took a knock in Barcelona's 2-1 win over Real Madrid last Sunday, he missed training with the team in Washington on Thursday.
Martino said that even though the tests showed no cause for concern, Messi continued to feel discomfort.
"In training on Friday he tried to work out and could not," he said. "Therefore we prefer not to play him. We're not going to risk a player. In the same way, I cannot guarantee you he will face Ecuador in three days."
Messi's Barca team-mate Javier Mascherano was also omitted from the starting line-up.
They saw a clear chance go begging in the second half, with in-form Juventus star Carlos Tevez firing wide two minutes before Banega's long range effort struck El Salvador's Nestor Renderos and flew past Salvadoran keeper Derby Carrillo to give the World Cup runners-up the lead.
Mancuello, who replaced struggling Manchester United star Angel Di Maria with 17 minutes to play, made a quick impact with his swinging effort that dropped into the far corner.
"I think the most important thing about this game is that Argentina eventually found a way to play without worrying about the outcome," Martino said.