The Barcelona star said the players' thoughts were with their coach, who will fly to Argentina following the death of his father.
The Blaugrana boss was present at Camp Nou for the victory over Frank de Boer's men in the Champions League, but he is scheduled to fly to his native Argentina following the death of his father, Jorge.
Messi, who followed in the footsteps of Cristiano Ronaldo's hat trick for Real Madrid on Tuesday by firing three goals in the win over the Dutch giants, says the performance was for the club's grief-stricken manager.
"We played better in the second half. It's a matter of time, we are adapting ourselves to the season," the 26-year-old told Canal +. "It's good to have alternatives. We have got many players who can do different things and can make the most of being given a chance.
"We want to dedicate it to Martino because he's not living a good moment now."