Will Grigg's 79th-minute goal gave Paul Cook's League One side a remarkable upset triumph, ending City's hopes of an unprecedented quadruple in the process.
While the post-match headlines were dominated by crowd disorder and a confrontation between the two managers, back in Manchester the Premier League leaders need to pick themselves up quickly for Sunday's Carabao Cup final.
In the second half, City laboured in their attempts to break down Wigan, who seemed to recommit to the idea of simply keeping out their opponents.
Wigan approached the second period with similar industry to the first and for a while they kept City at bay, until Guardiola chose to introduce Kevin De Bruyne 25 minutes from time.
"We certainly wish them well fighting on all fronts because they represent English football so well".
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Although Woods is now out of proceedings, Northern Ireland's Graeme McDowell holds a joint-lead going into the weekend's action. Moore opened his round with an eagle on the par-5 first hole and a birdie on the par-4 second.
It has now been claimed by The Mirror that the incident was started when someone spat at the Man City striker.
Once the City players had departed the pitch, a group of Wigan fans headed towards the away supporters section, resulting in violent scenes as City supporters attempted to get onto the pitch after being taunted by the home fans. This was the third time in six seasons that Wigan have defeated City in the FA Cup, their most memorable match being the 2013 victory in the final of the competition.
"Is a red card, yeah", said Guardiola.
"I sort of gambled and found myself in a foot race with Kyle Walker, which is not exactly ideal", he said.
Referee Anthony Taylor initially pulled the yellow card out of his pocket and then appeared to change his mind.
Sergio Aguero is restrained by a Wigan player and a Manchester City staffer during a brief altercation with a Wigan fan. It's safer when the fans are not there but sometimes it happens.
Chief Superintendent Stuart Ellison of GMP's Territorial Commander for Wigan, said: "Football is a family event and the disruption that players and fans alike faced last night will not be tolerated".