First-half goals from Kenwyne Jones and Jermaine Pennant were conceded far too easily and further defensive weaknesses were exposed after the break as we got ourselves back into the game late on only to throw it away seconds later.
Robin van Persie hit his 19th in his last 21 matches, the eighth time in succession he had scored away from home, with less than 10 minutes remaining only for Jon Walters to go straight down the other end and make it 3-1.
It was a defeat which put the top of the table beyond reach, although in truth we'd blown their chances of ended a six-year wait for a trophy several weeks ago.
Much of the pre-match focus had been on the return of Aaron Ramsey to the ground where he horrifically broke his leg in two places last season and a first meeting with Ryan Shawcross, the player whose tackle inflicted the injury.
As a result, despite Stoke's short time in the Premier League, these two sides have managed to build up plenty of history, with Wenger heavily critical of what he perceives as Stoke's over-physical style.
But the more relevant history related to Stoke's threat from set-pieces and our tendency to concede soft goals.
Both were prevalent at the Britannia Stadium and contributed significantly to the result.
Their problems were mainly all of their own making, typified by the opening goal which was scored with far too much ease.
Goalkeeper Wojciech Szczesny had already flapped at one cross which Pennant hooked wide when he was left totally exposed by his defence in the 28th minute.
Andrey Arshavin's needless push on Pennant close to the corner flag allowed the winger to clip over a free-kick and Jones, having evaded Johan Djourou far too easily, simply jogged in and let the ball hit him on the chest to divert it over the line.
The lack of effort required by the Trinidad and Tobago international to score against the league's third-placed side was embarrassing and Jones, presumably surprised by such a gift, did not even celebrate.
We should have been ahead well before that point though as the usually prolific van Persie blazed over from 10 yards when put through by Ramsey's through-ball.
Stoke fans' chant of "1-0 to the rugby team" was aimed at Wenger but the only direct thing about Stoke's second was the run of Pennant.
Cutting in from the left he was allowed to advance unchallenged and when Djourou belatedly came to meet him the winger fired in a shot which deflected off the defender and over Szczesny.
We were spared further embarrassment by the crossbar just before the break when Walters shot from a narrow angle on the left of the penalty area.
Strikers Nicklas Bendtner and Marouane Chamakh replaced Ramsey and Arshavin for the second half but it was the other end of the pitch where we were lacking as within seconds of the restart Robert Huth headed over Pennant's corner.
In the ensuing melee Alex Song appeared to catch the defender in the face with an elbow which went unnoticed by referee Mark Halsey.
There was greater concern for Huth when he suffered an injury scare six days before the FA Cup final, limping off with a knee problem.
For all the complaints about host's approach to the game, Bendtner was the first player to be booked when he upended Pennant close to the touchline, although the Stoke winger soon followed into the book for his retaliation to Jack Wilshere's studs-up challenge which also earned him a caution.
As the match entered its closing stages chances came at both ends; Begovic launching himself at Van Persie's feet to block an almost-certain goal and Glenn Whelan forcing Szczesny to tip his shot around the post from a counter-attack.
But with nine minutes remaining Begovic's slip up in allowing van Persie's shot to roll underneath him gave us a glimmer of hope.
But, true to form, a minute later Djourou's miserable afternoon was complete when his half-clearance fell to Walters who poked home.
Stoke still have a cup final to look forward to, for Arsenal there is only next season.