While content with the win, the Argentine stated the Blaugrana just are not the same without their talisman
The Brazilian opened the scoring from the spot on the half hour mark and netted the winner in the second period after Mateo Musacchio had levelled for the visitors shortly after the break.
But even though the likes of Alexis Sanchez shone in Messi's stead, Martino lamented the absence of his compatriot, who has been ruled out for the remainder of the year through injury.
"Losing or winning, we always miss Messi. He's the best player in the world. With him, we would have played even better today," he told reporters after the match.
"Preparing for the Getafe game without Messi and Neymar [through suspension]? We'll miss the best in the world and one who's among the top five, but we'll have to win anyway."
Martino nevertheless expressed satisfaction that his men played out the win on the same weekend title rivals Real Madrid could only draw against Osasuna.
"The team is getting better. It's almost a shame the winter break is coming. I almost wish they postpone the holidays," the coach continued.
"Following the Super Cup against Atletico Madrid, this is the game I'm most satisfied with because we continued at the levels shown against Cartagena and Celtic.
"This was an important game. I thank the fans for their support today, they were great for the entire game."