Andrey Arshavin marked his return to the side by finding the net in the fourth minute but the Russian's effort, after Van Persie's pass, was ruled out by an offside flag.
DID YOU KNOW?
This was the first time in six years Arsene Wenger picked an Arsenal team without a Frenchman in it
Van Persie went into the game looking to add to his stunning return of 12 goals in eight league and cup matches, yet it was Ramsey who was presented with Arsenal's best two chance of the first half.
The Wales international cut a frustrated figure when Schwarzer, who almost joined Arsenal last year, produced an excellent save to keep out his powerful eighth-minute effort following a sweeping three-man move involving Alex Song and Van Persie.
Then Ramsey spurned a glorious chance when he fired high and wide in the 24th minute after good work by Walcott.
England international Walcott struggled to stamp his authority on proceedings but he did manage to test Schwarzer in the 26th minute - one of the few saves the Fulham keeper had to make before the interval.
Fulham have established a reputation as notoriously poor travellers in recent seasons yet Martin Jol's side had their moments, with Moussa Dembele proving a real menace to the Gunners defence.
The former AZ Alkmaar player saw his 20-yard attempt in the 33rd minute deflected behind for a corner, from which Brede Hangeland headed narrowly wide.
And Dembele took advantage of some sloppy defending to force Wojciech Szczesny into his only serious save of the first half.
Arsenal needed to improve in the second half but they endured more frustration.
After Van Persie cleverly created room for himself inside the Fulham area on the hour mark, the striker let fly with a shot which was heading for the net before Baird did well to clear off the line.
Away point please Jol
Five minutes later Fulham were ahead.
A sublime ball by Murphy bounced off Riise's chest inside the Arsenal area and Vermaelen could only watch as his attempted clearance somehow ended up in the back of his own net.
Suddenly the Cottagers were within sight of their first ever win at Arsenal.
And when Schwarzer, who had an outstanding game, produced another excellent save to deny Djourou following a corner, it looked like Arsenal's luck had run out.
But with eight minutes remaining Vermaelen headed home Walcott's right-wing cross to lift Arsenal above Liverpool into sixth spot.
Arsenal manager Arsene Wenger said:
"Our pace was not right, but we've given a lot in recent weeks and went into this on the back of an intense Champions League match.
"It feels a little bit like a defeat because we've dropped two points and conceded a stupid goal. But I can't be too demanding on the team because the players are exceptional.
"I said before the game that Fulham are a good side and I haven't changed my opinion after this."
Fulham's Moussa Dembele said:
"If you watch us play every game then you will see we play well, but it's just the points that are missing.
"So I'm not worried about our position in the table, particularly after this performance and result.
"We knew it was going to be a difficult game coming to the Emirates but we're happy with the outcome, although we would have been happier with all three points."
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