Barcelona trailed 2-0 by the break and although it rallied behind Xavi Hernandez's penalty soon after the restart, it never sustained the pressure despite playing against 10 men for most of the second half.
"It didn't look like we were there in the first half. There was a lack of intensity, a lack of hunger," Fabregas said.
Martino did not beg to differ with his players.
"In a Champions League game, against a rival that is playing to reach the next round, you need to play with intensity for 90 minutes," Martino said. "We need to analyze, above all, the difference in intensity between the two sides. We cannot allow ourselves to play a first half like we did last night."
Apart from missing Messi, Barcelona was also without Dani Alves, Jordi Alba, Adriano, and goalkeeper Victor Valdes. Alves, Alba, and Adriano all trained separately from the squad on Wednesday, as did Xavi.
Barcelona has already qualified for the last 16 but could have clinched top spot in the group.
Instead, it will have to try again in the final round of the Champions League group stage when it plays Celtic at its Camp Nou stadium. Celtic will finish last in the group, regardless of the result.
"If we want to win in Europe, we cannot come out like that," Puyol said. "Our idea is to dominate possession, but when you are playing a team that also knows how to hold on to the ball and can bite, this is what happens."
Barcelona next plays at Athletic Bilbao in the Spanish league on Sunday.
