Arsene Wenger's side had already irritated the Emirates Stadium faithful by squandering a two-goal lead in a 2-2 draw against Boca Juniors on Saturday and another frustrating result triggered an angry response from the 60,000 crowd in north London.
Robin van Persie gave Arsenal the lead just before half-time, but the Gunners wasted several opportunities to score again and their porous defence conceded a host of chances before New York finally equalised through a Kyle Bartley own goal in the final minutes.
The draw was enough to leave New York as winners of the four-team tournament, which also featured Paris St Germain and Boca Juniors.
It was another dispiriting day for Wenger, who has been heavily criticised for his failure to make top-class signings during the close-season after six years without a trophy.
To make matters worse England midfielder Jack Wilshere was forced off with an injury after just seven minutes.
Arsenal's current malaise is a far cry from the glory days of Thierry Henry, who was treated to a hero's welcome on his return to the Emirates with New York.
The Gunners' record goal-scorer took only seven minutes to make an impact as he drove a low shot just wide.
After Henry's free-kick forced an acrobatic save from Wojciech Szczesny, Aaron Ramsey missed a glorious chance to put Arsenal ahead, blazing over following Van Persie's rampaging run.
That didn't seem a major problem when Van Persie broke the deadlock in the 42nd minute with a header from Tomas Rosicky's free-kick.
But new signing Gervinho wasted a chance to make it 2-0 as the Arsenal forward shot too close to the goalkeeper.
Arsenal's habit of contributing to their own downfall with poor defending resurfaced as Henry was allowed a clear run on goal only to shoot wide in the second half.
Henry was the inspiration for New York's 84th minute equaliser as he threaded a pass to Juan Agudelo, whose cross was turned into his own net by Bartley.
In the day's earlier match Paris St Germain cruised to a 3-0 victory over Boca Juniors.
PSG lost their opening game 1-0 against New York on Saturday but the big-spending French club gave a much-improved display to brush aside their Argentine opponents.
Jean-Eudes Maurice punished poor defending from Boca to open the scoring in the early stages and Guillaume Hoarau headed the second goal just before the interval before Marcos Ceara's second-half free-kick sealed the victory.
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