Thierry Henry’s 80th-minute penalty ended Newcastle's resistance after the Magpies had twice fought back from behind.
Henry gave Arsenal an 18th minute lead but Laurent Robert equalised eight minutes later.
And, when Gilberto Silva put the hosts back in front in the second half, it took Newcastle less than five minutes to restore parity again through Olivier Bernard.
But Henry secured all three points for Arsenal from 12 yards after Jermaine Jenas's handball.
The Gunners remained one point ahead of Chelsea and Manchester United at the top of the table. Newcastle stayed 19th with three points.
Fernando Torres hit a hat-trick as Liverpool romped to a convincing home win over Hull City.
The Spaniard opened the scoring in the 12th minute and, despite Geovanni equalising, he struck again just before the half-hour mark and completed his treble less than two minutes after the break.
Steven Gerrard’s cross then evaded everyone and flew into the net, while Ryan Babel added a late brace.
Liverpool remained third but moved within three points of the summit. Hull stayed 19th with four points.