The decision should have been insignificant minutes later but William Gallas sidefooted embarrassingly high from point-bank range after Bacary Sagna flicked on a Gunners corner.
Arsenal's trademark fluent football was in full flow after a stuttering start to the season and it was proving too much for Newcastle to handle.
Wenger happy with positive performance
Magpies keeper Shay Given palmed away a long range powerful Kolo Toure strike before Arsenal's pressure inevitably reaped reward.
N'Zogbia was punished for blocking an Adebayor cross with his arm and Van Persie hammered in the spot-kick.
Newcastle would have to make the most of any chances they were afforded but failed to do so when a rare opportunity came begging.
Jonas Gutierrez crossed low into the Arsenal box and Owen - put off by team-mate Shola Ameobi - sidefooted wide in front of watching England boss Fabio Capello.
Arsenal resumed normal service as they continued to carve out chances and Eboue's creativeness set up Van Persie for his second.
Keegan hails 'breath-taking' Arsenal
The visitors improved after the break and Butt glanced a header against the crossbar but Arsenal heeded the warning and responded in style.
A triangle of Samir Nasri, Adebayor and Denilson combined to find a way through the Magpies defence.
Denilson added the finish with an angled shot before Van Persie lashed a strike against the underside of the bar, which bounced clear to Newcastle's relief.
Arsenal failed to add to their lead, despite a number of chances, as they eased to victory.
Newcastle boss Kevin Keegan brought on Joey Barton to a chorus of boos before the visitors' misery was ended.
Arsenal boss Arsene Wenger: "I'm very pleased with the performance, both offensively and defensively. It was a complete one, there was great balance in the team, with movement.
"Apart from at the start of the second half, we were always in control and played the game we love, and showed the way we can play.
"The improvement comes from a completely different attitude."
Newcastle boss Kevin Keegan believes Arsenal's Samir Nasri should have been sent-off for an off-the-ball incident with Joey Barton: "Joey came on, got a good tackle in on Nasri. Then the guy sliced him down," said Keegan after the 3-0 defeat.
"I like Nasri - he's a player we looked at for a possible signing but you can't do that.
"I know the referee didn't see it but the linesman did and it should have been a red card."
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