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The Serie A leaders, beaten 3-0 by Lille in the previous Group H game, restricted the hosts to just 42 per cent of the ball only to concede from their only shot on target of the second half.
Similarly, AC Milan found the net with their one effort on goal in the 90 minutes, as the absence of the injured Ibrahimovic appeared to take its toll.
The 39-year-old, who sustained a hamstring injury after scoring a double in the 3-1 win at Napoli, has scored 12 goals in as many games in all competitions this season.
Still, Milan havewon six and drawn four of their 10 games without Ibrahimovic in 2020, and Bonera says that level of resolve was once again apparent against Lille.
"This is the strong identity we now have in all of us. We're happy with the work the boys do every day. It's just a shame about the result tonight," said the assistant coach, who is deputising for head coach Stefano Pioli while he self-isolates after a positive coronavirus test.
"We showed even before this match that the group was able to make up for his absence. He is such an important player, but the spirit of this team is always the same, with or without Ibra."
Young playmaker Sandro Tonali was also frustrated that AC Milan could not hold onto three points, but he said they proved they could play well without their main striker.
"We deserved to take the lead. We didn't dominate but we held onto the ball like a great team, and that's our biggest regret –not being able to win," he said.
"Playing with Ibra certainly helps; with a champion like him, it's always easier. But we have to play well even without him and we've shown we can play as a great team."