Goals from Neymar and Alexis Sanchez secured Barcelona a ninth win from 10 games in La Liga this season, with Jese scoring a late consolation for Real.
Martino's Real counterpart Carlo Ancelotti was unhappy that a penalty was not awarded for Javier Mascherano's second-half challenge on Cristiano Ronaldo, but the Barcelona coach refused to comment on that decision.
Instead, he felt his side had started the game well but dropped off towards the end, and he also compared the team's performance as a whole with Lionel Messi's.
"We played well at first but tailed off, and the same is true of Messi," said the Argentinian coach.
"But he worked hard and I rate his performance. If he, and the other players, can continue playing this well, we're going to have a good season."
Barca moved six points clear of Real at the top of the table and four points above Atletico Madrid, who play Real Betis on Sunday.
But Martino was careful about saying what effect the result would have on the title race, commenting: "The victory is good for our spirits, and is more important in that sense than mathematically.
"There is still 60 per cent of the league season left, and Madrid and Atletico are close to us, they can still make up the difference."