Gunners manager Arsene Wenger was given the option of returning to London without a ball being kicked in anger in Group H after a partial floodlights' failure left a corner of the pitch in relative darkness.
But the Frenchman agreed to play the match and his faith was justified although a bunch of missed chances meant his team made hard work of seeing off Partizan who played the last half-hour without Marko Jovanovic, sent off for a last-man foul.
Andrei Arshavin had fired Arsenal ahead in the 15th minute with a fine solo effort but Partizan, roared on by 30,000 fans, equalised against the run of play when Cleo converted a penalty after Denilson had handled an innocuous cross.
Partizan keeper Vladimir Stojkovic then pulled off a string of superb saves, including a 57th-minute penalty stop from Arshavin, who could have had a hat-trick by half-time.
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But the hosts could not hold on after Jovanovic was shown the red card for a last-man foul on Marouane Chamakh which led to the spot-kick.
Much to the evident relief of Wenger, Chamakh restored Arsenal's lead with a 71st-minute tap-in after Alex Song's shot from inside box rebounded off the post.
"I was concerned after we missed the penalty but I also felt we had enough time to score the second goal and I thought we looked very comfortable after we got it," Wenger told a news conference.
"Partizan gave us the game we expected, fully committed and powerful on every break. We had a lot of the ball and created many chances so overall I am happy with the performance.
"We couldn't kill the game off after they came back with a penalty so we needed to keep the pace high and be patient to score the second goal," he added.
With Partizan running out of steam, defender Sebastien Squillaci headed in the third from a Samir Nasri corner to seal Arsenal's second successive group win, following a 6-0 home drubbing of Portuguese side Braga.
Cleo, who took his Champions League tally to nine goals in eight games, missed a late penalty and substitute Ivica Iliev also spurned a good chance to reduce the arrears when Lukasz Fabianski parried his close-range shot.
With one eye on a trip to London rivals Chelsea in the Premier League on Sunday, Wenger was also relieved the game went ahead after multiple floodlight failure caused by an electrical hitch threatened to have the kick-off delayed or even abandoned.
"I thought it would have been terrible to go home and not play so I encouraged UEFA when they asked me if we wanted to play with one (floodlight) corner off," he said.
"I said yes as long as the referees were happy with it and overall it was acceptable but I really don't know what happened.
"I believe we will go to Chelsea with the desire to do extremely well because we know how big a game it is for us."
The game was played under tight security amid fears of crowd trouble but Wenger praised Partizan's fans, who gave their team a standing ovation after the final whistle.
"They were supportive but not aggressive. They crea
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