Thierry Henry and Dennis Bergkamp offered Arsenal's best chances but both were denied by saves from United keeper Roy Carroll.
Van Nistelrooy's goal silenced his critics following his error in a match against Manchester United last year when he missed a last minute spot-kick at the same fixture 12 months ago.
Magpies triumph
Shearer scores
Elsewhere in the Premiership Newcastle United beat Manchester City 4-3.
In an exciting match Craig Bellamy's superb flicked volley swung it for the Magpies.
Southampton won a point in a 0-0 draw against Birmingham.
The Saints went into the game missing lots of top players so their move off the bottom of the table and will consider it a worthy point.
Portsmouth have yet to win an away match this term and a 1-1 draw with Middlesbrough saw the wait went on.
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