Adriano's curling strike in the shadows of half-time was enough to secure the three points but it might not have stayed that way were it not for some poor Malaga finishing and a strong performance in goal from Victor Valdes.
Without the injured Lionel Messi, Martino said his players lacked their usual rhythm, particularly in the second half.
"At times we weren't as effective as we could have been," Martino said.
"In the first-half we had chances and control of the game, but we couldn't maintain the same control of the ball in the second-half and they had two clear chances, one against the post and the other that Victor managed to save.
"We didn't take advantage of the times when we had space in the second-half."
Neymar started his third consecutive game on the bench - despite Messi's leg muscle injury ruling him out of the contest - and the tricky Brazilian was again lively as he gradually improves his match fitness.
"You can already see the difference in (Neymar) between the last two matches and the first league match against Levante," Martino said.
"I don't know when exactly we will decide to start him but you can see mentally he is ready and we will do it at the most opportune time.
"He only played half an hour but he was always doing positive things for the team."
Meanwhile, Martino was defiant in his continued verbal battle with Real Madrid manager Carlo Ancelotti over the Gareth Bale transfer.
The Barcelona coach reiterated his comments that Real Madrid 'lack respect' for society because of the amount of money offered for Bale despite Ancelotti retorting that Martino lacked an understanding of football.
"I said what I said about Bale and his price," Martino said.
"It's not for any personal confrontation with Ancelotti.
"(The Bale transfer fee) doesn't seem appropriate and I'll stick with what I said in the week - I'm not retracting it."
