The 22-year-old faces at least six weeks of rehabilitation, and a further two before being up to full match fitness, after tests showed he had sustained a hairline fracture in his left foot.
The damage followed a hefty tackle from Liverpool defender Daniel Agger early in England's friendly against Denmark at Wembley on Wednesday.
Wilshere played on following treatment until he was replaced on the hour, and when speaking to reporters afterwards maintained it was "just a bruise" having been initially assessed by the Football Association medical staff at the stadium.
Arsenal confirmed the full diagnosis following consultations with an independent radiologist.
Should all go to plan, then Wilshere could be back in time for the final two Barclays Premier League matches - and possibly an FA Cup final date if the Gunners progress, with Saturday's quarter-final tie against Everton their next fixture.
England manager Roy Hodgson, who is set to name a provisional 30-man World Cup squad on May 13 - has already expressed his sympathy for both player and club.
Wenger remained pragmatic today as he said: "I had no agreement (with Hodgson over Wilshere's game time), no
It is an accident on a good ankle.
"I think the tackle was strong, but I think he (Agger) wanted to go for the ball."
Wenger indicated he would probably have done the same in allowing Wilshere to continue once the midfielder - who had looked in considerable pain initially after the impact - was back on his feet.
"It is the pain of the player that gives you the indication and you trust always the player," he said.
"Sometimes you give him a few minutes when a guy has been touched like that to tell you how he feels and if there is no pain we are not at the point where you can make an instant check up (on the pitch) with X-rays to see how big the damage is.
"Most of the time, it is the indication of the player that helps you if you can go on or not."
Wilshere has endured fitness issues since first suffering an ankle problem in the build-up to the 2011/12 campaign, and spent 17 months on the sidelines which saw him miss out on the chance to play at both the European Championships as well as represent Team GB at London 2012.
Wenger, though, is confident the 22-year-old has the strength of character to recover once more.
"He's in the boot and he's gone away for a few days to get a little bit away from travelling and the disappointment and think about something else," Wenger said.
"We want to help him come back as quickly as possible and prepare for the rest of the season."
Elsewhere, France defender Laurent Koscielny faces a fitness test on a hamstring problem also sustained while away on international duty so captain Thomas Vermaelen is on standby to deputise
Full-back Nacho Monreal (ankle) will also be assessed as Wenger looks to utilise his squad
Forward Steven Naismith believes Everton have no reason to fear Arsenal as they have proved this season they are a match for the big teams
Roberto Martinez's side head to the Emirates Stadium for a match which could have a major bearing on the remainder of their season.
Having dropped nine points off the pace - discounting fourth-placed Manchester City's two matches in hand - in the race for Champions League football, the FA Cup represents their best chance of success even if European football remains a possibility
Having gone to the Emirates in December and earned a creditable 1-1 draw Naismith thinks the trip south can be made with confidence even if their away record in terms of results against their rivals is mixed
Everton suffered their first league defeat at Manchester City in October and have lost at Anfield and, less deservedly, at Tottenham but did register an historic victory at Manchester United four days before their draw at the Emirates
"It is a massive game," said Scotland international Naismith
"You need to beat the big teams if you want to get to finals and win trophies so we are going to work hard
"
Arsenal had an unexpected defeat at Stoke last weekend which dealt a blow to their title hopes, but Martinez does not think that will have much bearing on Saturday's encounter
"There is never a good or bad time to face a top team
We admire Arsenal immensely for the team they are," he said
"They had a disappointing result at the weekend but that does not change anything
"They can perform without looking at what happened in the previous game
"They are as good as anyone when they get on the ball and have free movement
"But if you want to be winning a competition like the FA Cup you have to find a way of being effective against a team like Arsenal
"We need to replicate the level of performance we had at the Emirates earlier in the season
"I thought first half we played really well but when you are dominant you need to reflect that in the scoreline and that is where we need to improve."
Goalkeeper Joel Robles is set to continue his FA Cup run in the side by replacing Tim Howard
Captain Phil Jagielka is unlikely to feature having missed last weekend's win over West Ham and England's midweek friendly with a hamstring injury but fellow centre-back Antolin Alcaraz is fit again after six weeks out with a muscle problem
On-loan striker Romelu Lukaku is set to start having come off the bench to score the winner against the Hammers
Source : PA
Source: PA