Steve Cotterill's side had seen MK Dons climb to the summit with a 5-0 demolition of Crewe Alexandra on Saturday, but they responded strongly to regain first place.
Matt Smith opened the scoring seven minutes into the second half when he turned in Joe Bryan's cross from close range.
Jay Emmanuel-Thomas sealed the victory in the final minute as City restored their two-point advantage at the top.
Elsewhere, Walsall drew 1-1 at home with Gillingham.
Bradley Dack gave Gillingham the lead in the 69th minute, but parity was restored five minutes later as Ashley Grimes struck to draw the hosts level and secure a share of the spoils.
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