Nasri (left) and Walcott produced the goals to ease Arsenal nerves
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Arsene Wenger knew that three points would assure them of qualification for the knockout phase and they ultimately ran out comfortable winners, although for a spell in the second half against the Serbians, there was the fear that Arsenal's proud record might end.
Arsenal's win was not enough to give them top spot in Group H, and they now face the prospect of running into the real elite of European football when the draw is made on 17 December.
Robin van Persie, Arsenal captain on his first Champions League appearance of the season, put them ahead on the half-hour from the spot after he was fouled by Marko Jovanovic.
Partizan's only moment of serious danger brought an equaliser just after half-time when Cleo's shot took a wicked deflection off Sebastien Squillaci and out of Lukasz Fabianski's reach - leaving Arsenal's fans, albeit briefly, anxiously following events in the game between Shakhtar Donetsk and Braga.
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Wenger unsure how far Arsenal can go
He restored Arsenal's lead with a fine volley after 73 minutes, and another moment of class from Samir Nasri wrapped things up as he scored with a fine low finish four minutes later.
Arsenal suffered a blow with an early injury to defender Kieran Gibbs, while Bacary Sagna was shown a red card in the closing stages for a foul on Aleksandar Lazevski.
Wenger will be delighted with Arsenal's win, but he will know they will need to produce better in the knockout stage - a task that will be made much easier by the return of injured captain Cesc Fabregas.
Before the game Arsenal knew that victory would ensure their passage to the knockout phase - but they made a lacklustre start despite dominating possession and territory.
Wenger was also forced into a change after only 24 minutes when the desperately unlucky Gibbs suffered misfortune again. He was stretchered off after slipping as he made a tackle, and despite trying to carry on he was eventually replaced by Emmanuel Eboue.
Van Persie won the penalty he converted to put Arsenal ahead
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Arsenal keeper Fabianski had been a virtual spectator, but he was powerless to stop Partizan scoring a shock equaliser seven minutes after the break when Cleo broke through and scored via a big deflection off Squillaci.
Wenger needed to inject urgency into Arsenal as they flirted with an early Champions League exit, and his answer was to send on Walcott, a move that brought the required result.
He put Arsenal back in front and eased growing concern inside The Emirates with an instinctive right-foot volley that flashed across Partizan keeper Vladimir Stojkovic into the far corner.
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The night ended on a low when Sagna received his red card, but Wenger will insist this was simply a case of Arsenal getting the job done - which they eventually did.