Messi failed to contribute much during his time on the pitch in the first leg of the Spanish Super Cup final, and was replaced by Cesc Fabregas immediately after the re-start, at which point Atletico led 1-0 thanks to a stunning volley by former Barcelona player David Villa.
Martino's side improved after the break, and levelled after 66 minutes when Neymar headed in a cross from Dani Alves, scoring his first competitive goal for the Catalan club.
Martino took Messi off in the second half of Barcelona's 7-0 win over Levante at the weekend to give the player a rest, but said on this occasion he substituted the forward because he was injured.
He told a press conference: "Messi picked up a knock and when a player has an injury or a knock which impedes them from playing it does not make much sense for them to stay on the pitch."
Martino admitted his side had struggled at the Vicente Calderon, saying: "All of our players found it difficult to find space to receive the ball. We couldn't play between the lines, they kept very tight on us and it was difficult to get past them. They were better in the first half, we were better in the second."
The most controversial moment of the game came midway through the second half when Sergio Busquets brought down David Villa but was not shown what would have been a second yellow card.
However, Martino did not think his midfielder deserved to be sent off.
"I'm not sure, it was a normal foul to me, I'm not convinced it deserved a yellow," he said.
Atletico boss Simeone also refused to criticise referee Alberto Undiano Mallenco for the incident, remarking: "If the referee didn't think it was a yellow card then he was right not to give it."
But Villa was not so sure. He told Television Espanola: "It was a key decision to not give a second yellow card to Busquets, especially because of the amount of yellow cards we received in the first half. He let him off the hook.
"It would have been crucial, because we would have had an extra man while leading 1-0. But referees are human and sometimes they get it wrong."