Television cameras picked up Wilshere raising his middle finger in the direction of home 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."
Source: PA
Source: PA