Four-time Ballon d'Or winner Messi is yet to start a competitive match since tearing a hamstring at the start of November, although he scored twice after coming on as a second half substitute in Barca's 4-0 win over Getafe in the Copa del Rey in midweek.
He played 45 minutes against Atletico, replacing the injured Andres Iniesta.
Neymar, meanwhile, was forced to miss the Getafe game with gastroenteritis and did not appear at the Calderon until the 66th minute, coming on for Alexis Sanchez.
Although Messi glanced a header wide of goal and forced a save from Atletico goalkeeper Thibaut Courtois, neither player had the desired impact in what was a tight game between Spain's top two.
"They weren't ready to start, any other coach would have done the same," insisted Martino in the post-match press conference.
The Argentinian coach admitted that the injury to Iniesta forced him to give Messi more minutes than he had planned, but thought his compatriot did well in the circumstances.
"We were thinking he would play less of the game than he did, but he looked sharp and created two chances," he said.
"Atletico also made things uncomfortable with him.
"It's my job to take decisions like this and I think it was for the best.
"Neymar had a stomach problem before the Getafe game and that always makes you weaker.
"We know Messi scored two goals (against Getafe) but we shouldn't forget that he was inactive for the first 60 minutes."
Barca remain top of the Primera Division and ahead of Atletico on goal difference at the half-way point in the season, and Martino reflected: "A point here is good, even though we wanted to win. We were up against a team that picks up a lot of points, we created chances and joined in the fight.
"Being top after the first half of the season with 50 points isn't bad. We've picked up a lot of points although we haven't played well in every game, but we're getting better and will improve as the season goes on."