The game ended goalless, ensuring Qarabag slipped to third and crashed out of the competition, but the hosts gave Inter a scare when they had the ball in the net late on only for it to be ruled offside.
With Inter already ensured of top spot in Group F, Mancini opted to name a youthful side with Yann M'Vila and Pablo Daniel Osvaldo among the few senior members.
Despite failing to take maximum points, Mancini felt his team performed well and urged them to now turn attentions to arresting their Serie A malaise against Chievo on Monday.
"I'm happy because the team has put together a great performance, even with three or four young boys," he told Mediaset.
"We lacked only a goal. It was a tough match and difficult because they wanted to win at all costs.
"It was a useful trip. Now, however, our attentions should go to Chievo and hoping that things will go better.
"We must improve further and to gather points quickly."
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