Wednesday - who didn't have one player in their side with first team experience - went ahead through Nathan Styles in the 32nd minute with a close range goal.
City also fielded a totally youthful starting eleven, and restored parity just three minutes later as Liam Cattermole scored from the rebound of Michael Byron's shot that hit the bar.
Ben Burgess was brought on at half time to make his second appearance in a week. He should have scored soon after coming on, but somehow shot wide of the open goal after rounding the keeper.
The home side went back in front in the 69th minute when Kyle Fores-Chambers was gifted a goal from Tom Matthews' underhit backpass.
City had no reply, meaning that they lost for only the second time in the league this season. They look to bounce back at Hartlepool next week.
City line-up: Richmond; Wiseman, Hotte, Byron, Matthews; Fry (Briggs), Anderson, Allanson, Benson (Burgess); Cattermole, Donaldson.
Un-used subs: Wilkinson, McGarry, Beattie.