He carried on but was clearly in discomfort and was replaced by Lukasz Fabianski with 12 minutes left.
An own goal by Fabianski gave Porto the lead on 10 minutes when he spilled Silvestre Varela's cross.
Sunderland almost took the lead after 14 seconds but Carlos Edwards' volley was well parried by Lukasz Fabianski.
Goalkeeper Lukazs Fabianski appeared vulnerable throughout and is sure to attract some blame for both goals conceded by Arsenal.
Keeper Lukasz Fabianski picked up what was deemed a Sol Campbell backpass and Falcao scored from a quick free-kick.
The ball looped over Poland goalkeeper Fabianski only to clip off the top of the crossbar and out again.
And the home side almost made an explosive start but Fabianski stopped a cracking 30-yard half volley from Edwards.
Sunderland had the last word though and Fabianski had to get down well to stop O'Donovan's shot in the closing stages.
Alex ripped a 25-yard free-kick high past the despairing grasp of Fabianski after Koscielny had been booked for a foul on Anelka.
Since Fabianski's injury last month, youngster Wojciech Szczesny has started seven of Arsenal's last eight matches and impressed his manager in the process.
Arsenal teenager Mark Randall had a goal disallowed while Fabianski had to save well to deny Sunderland striker Roy O'Donovan in injury time.
Arsenal were instantly deflated, and Fabianski had to make fine saves from Michael Essien and Cole as Chelsea threatened to extend the victory margin.
The only scare for Wenger's side for the rest of the half was a 30-yard piledriver from Micael, which was pushed safely away by Fabianski.
Fabianski had firmly established himself in Arsenal's starting XI this season, taking over the number one role when Manuel Almunia suffered an ankle in September.
But after Rosicky was denied a penalty, Falcao poked in a Ruben Micael free-kick after Fabianski had picked up a backpass from Campbell inside the box.
Campbell, the centre of attention once again, appeared to pass the ball back to Fabianski and was shocked to see his keeper pick up the ball.
Anelka robbed the hesitant Sebastien Squillaci, and even though the striker rounded Fabianski the angle was too acute and the finish rolled agonisingly wide for Chelsea.
The Spaniard was making his first league start since September in the absence of Wojciech Szczesny and Lukasz Fabianski, but there was no excuse for this howler.
Wenger refused to blame Fabianski, who was also criticised for displays in the recent FA Cup defeat by Stoke and last season's FA Cup semi-final loss against Chelsea.
Zewlakow scrambled the ball away, but from the resulting corner Arsenal stopper Fabianski had to get down smartly to his left to palm away Dave Edwards' goalbound shot.
The threat of Drogba hung over Arsenal like a cloud, however, and he posted the warning signs by forcing a desperate block from Fabianski with an angled drive.
Eastlands was emptying out by the time City launched a late rally, Adebayor almost latching on to a Silva pass and Fabianski tipping Boateng's drive over the bar.
And after Rodallega missed two early opportunities, the first a header, the second a low drive easily held by Lukasz Fabianski, it was N'Zogbia who created the opening goal.
But the turning point of the match occurred seven minutes after the break when Fabianski picked up the ball from what Hansson judged to be a backpass from Campbell.
The Poles also made several switches, with Celtic's Artur Boruc taking over from Fabianski in goal, while Ebi Smolarek, Guerreiro and Wojciech Lobodzinski replaced Rafal Boguski, Gargula and Krzynowek.
Porto looked intent on ripping the visitors apart and soon after Hulk, banned in the domestic league since December, blasted wide, the all-important opener arrived thanks to a shocking error from Fabianski.
No sooner had City almost opened the scoring - Lukasz Fabianski reacting brilliantly to keep out David Silva's goalbound flick from a Carlos Tevez cross - than they went down to 10 men.
On 19 minutes Bellamy played a one-two with Gareth Bale and hared away towards the Polish goal, only for the covering Michal Zewlakow to clear the danger as Bellamy chipped over onrushing keeper Lukasz Fabianski.
Dundee United's Lukasz Zaluska, who will join Celtic next season, could be in line for a place in the team for the Group 3 match in Kielce, while Arsenal's Lukasz Fabianski is also available to Beenhakker.
Fabianski again needed to be at his best to deny Silva from a tight angle, but from then on it was all Arsenal and Song swept into the top corner following a period of sustained pressure.
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