The Magpies' thrashing at Wigan opened the door for the Gunners to move six points clear and all but clinch a Champions League spot.
But they went behind after nine minutes at the Britannia Stadium when Peter Crouch rose above the defence to head in and, although Robin van Persie equalised six minutes later, they could not find a winner.
Arsenal boss Arsene Wenger made two changes from the team that drew with Chelsea last week, Gervinho and Yossi Benayoun replacing the injured Theo Walcott and Alex Oxlade-Chamberlain, while former Gunner Jermaine Pennant returned to the Stoke side.
The two clubs have history, most notably their clash at the Britannia Stadium two years when Ryan Shawcross was sent off for a challenge in which Aaron Ramsey broke his leg.
The atmosphere was spicy from the start, and Dean Whitehead was booked in only the third minute after catching Alex Song with his studs.
Arsenal had lost on three of their previous four visits to the Britannia, but they had two great early chances this afternoon, the first in the sixth minute when Van Persie played in Tomas Rosicky, but his shot lacked power and was held by Asmir Begovic.
The same duo combined moments later as Rosicky picked out Van Persie at the back post, and his header drew a terrific save from Begovic low at his near post.
Having survived those scares, Stoke went down the other end and took the lead with nine minutes gone, Matthew Etherington picking out the towering Crouch, who planted his header firmly past Wojciech Szczesny.
Arsenal hit back strongly and, after Ramsey had curled a shot just wide, they found the leveller in the 15th minute.
Stoke had not learned their lesson and again allowed Van Persie to run through the defence to meet a cross from Rosicky, and this time he made no mistake for his 35th goal of the season.
The visitors were well on top now and continued to threaten Begovic's goal, with Laurent Koscielny heading over the bar and Gervinho missing a cross completely six yards out before ending a fine run with a wild shot.
The loudest cheer of the day came from the Arsenal fans when the Newcastle scoreline was read out at half-time, but the visitors were grateful to Szczesny for some alert goalkeeping in the opening minutes of the second half as he twice punched away dangerous crosses, one from Etherington and one from Pennant.
At the other end, Van Persie got his head to a Bacary Sagna cross 10 yards out, but could not beat Begovic, while a jinking run from Rosicky was ended with a fine challenge by Shawcross just as the midfielder was about to shoot.
The first 20 minutes aside, there had been very few real chances for either side, but Arsenal were given a good shooting opportunity when Ramsey's turn 20 yards out was too sharp for Glenn Whelan.
Van Persie's shot was blocked by the wall, though, and Shawcross then did well to stop Thomas Vermaelen's follow-up, although Arsenal felt he should have been penalised for handball just outside the area.
The Gunners then appealed vociferously for a penalty when Benayoun went down under pressure from Whelan, but referee Chris Foy was unmoved.
Wenger sent on Abou Diaby, Marouane Chamakh and Andre Santos for Ramsey, Gervinho and Benayoun, while Pennant was replaced by Cameron Jerome for Stoke, and he was into the action immediately with a shot beaten away by Szczesny.
Vermaelen tried his luck from another free-kick, but screwed it wide, while at the other end a long throw from substitute Rory Delap had Szczesny in all sorts of trouble, but Sagna cleared from virtually off the line.
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