The coach, who was sent to the stands at half-time, saw his side slip to their third La Liga defeat of the season and allow rivals Real Madrid to open up a three-point lead at the top of the table.
Barca, who gave a rare start to Alex Song, were far from their fluent best and were punished in the 32nd minute when the Cameroon international diverted a Gorka Elustondo header into his own goal.
When Lionel Messi levelled four minutes later Barca looked well set to go on and win the game, but two goals in five second-half minutes saw Sociedad come out victors.
Martino confessed that he made changes too late in the game as he reacted to going behind rather than bringing fresh legs on while the scores were level.
"Real played well but the reading (of the game) I did was not right," he said. "I thought we had to run a little more to get the win and the best thing to do was what we did in the second leg of the Copa del Rey.
"I thought the Messi goal put us in the game, but not making a change before their two (second-half) goals came was wrong.
"We needed to rethink the way they play and when decided to make the first change it was 3-1.
"We have to look forward."
The defeat means Barcelona could drop to third if Atletico Madrid avoid defeat on Sunday against Osasuna, while Sociedad climb into fifth above Villarreal.
On the incident that saw him sent to the stands, Martino added: "About my sending off, I don't have anything to say. The ref made a decision and it's just that."
