Television cameras picked up Wilshere raising his middle finger in the direction of Manchester City supporters at the Etihad Stadium during the second half of the Gunners' 6-3 Barclays Premier League defeat on Saturday.
Although the incident was missed at the time by referee Martin Atkinson and his officials, the FA was able to retrospectively implement disciplinary proceedings against the player under a new pilot scheme for 'not seen' incidents in Premier League matches.
As such, an independent three-man panel agreed if the gesture had been viewed during the game, then it would have merited a dismissal.
Arsenal submitted mitigating circumstances to the governing body, arguing the length of the punishment is excessive, but those submissions were rejected and so Wilshere will now miss both the visit of Chelsea on December 23 as well as the Boxing Day trip to West Ham.
A statement from the FA read: "Arsenal's Jack Wilshere has been suspended for two matches by an independent regulatory commission.
"Wilshere was charged by the FA with making an offensive and/or insulting and/or abusive gesture during the fixture between Manchester City and Arsenal at the Etihad Stadium on Saturday 14 December.
"The incident was not seen by match officials, but was caught on video.
"Whilst admitting the charge, Wilshere claimed the standard sanction for this offence was clearly excessive. The commission rejected this claim and the two match suspension will commence with immediate effect."
In December 2011, Liverpool striker Luis Suarez was suspended for one match, fined £20,000 and warned as to his future conduct after he made a gesture to home fans as he walked off the pitch following a 1-0 defeat at Fulham.
However, a precedent had been set from earlier this season when a two-match suspension was handed out to Blackpool winger Tom Ince after he was retrospectively charged in relation to a gesture towards a match official in a Capital One Cup tie against Preston.
FA chairman Greg Dyke had earlier empathised with the player's frustrations, but insisted the highest examples must always be maintained by the professionals on the pitch and Wilshere, who turns 22 on New Year's Day, must take lessons on board.
"As a supporter I sympathise with the players because of the flak they get from the crowd," Dyke said on talkSPORT.
"People can lose their cool very quickly, but he (Wilshere) has got to learn. He's very well paid to play the game and he's got to learn to cope with it.
"You think back over many years of players who were hot-headed when they were younger, but not when they get older. They just learn and mature. That is what happens. It is part of life."
Arsenal will need to respond from their drubbing at City to avoid potentially being pushed down into fourth place for Christmas should all the results go against them this weekend.
Defender Laurent Koscielny remains a doubt for Monday night's showdown with Chelsea after he suffered a deep gash in his knee just before half-time at the Etihad Stadium.
German forward Lukas Podolski, however, could be involved for the first time since late August following his recovery from a hamstring tear.
Midfielder Alex Oxlade-Chamberlain has targetted a return early in the new year having suffered a knee injury in the first game of the Premier League season against Aston Villa.
The 20-year-old England World Cup remains hopeful of a positive recovery, just as midfielder Aaron Ramsey has shown is possible after breaking his leg in two places during February 2010.
"You can either let setbacks be a setback or let them be a temporary setback as part of a learning curve to go on and turn it into something positive," Oxlade-Chamberlain told Arsenal Player.
"People sometimes don't realise if you get an injury like that, doing something you do on a day-to-day basis and sometimes you can't put your finger on why it happened, to come back from that and put yourself under threat of doing that same horrific injury that brings back those bad memories again, that can be really challenging mentally.
"I think the way that Aaron has come back from that injury and a time like that to show what he is doing this season and even in the seasons before, ever since I have been here, he has been a brilliant player and I can say the same about Jack (Wilshere) with his injury as well.
"The amount of time he was out and to come back and see how positive he is now and how hard he is still working to make sure he tries to prevent injuries like that again, is a real learning curve for any player.
"For me, now I find myself in the same situation they found themselves in, hopefully on a shorter length of injury, it does give you hope.
"You can take a lot of positivity from that and confidence that you can come back stronger."