Chester had their new goalkeeper Stephane Gillet sent off as they crashed to a seventh straight league defeat.
With 20 minutes to go he chased outside his area for a tackle on Junior Agogo which left the Rovers striker needing treatment.
Rovers were already 2-0 up and David Artell, who took over in goal, did well to stop them scoring again. In fact Chester were able to pull back a late goal through lively sub Ben Davies.
The win confirmed Rovers' rise under Paul Trollope and was revenge for a 4-0 drubbing at Chester in September before the sacking of manager Ian Atkins.
Sammy Igoe, who has arrived at Rovers on loan from Millwall, should have put his new club in front after nine minutes.
He was through with a clear shot and just a few yards out, but Luke Dimech slid in to Chester's rescue, leaving City to defend two corners.
The second was fatal, Stuart Campbell hit a deep cross to the far post which saw Christian Edwards outjump them all to score on his first start since August.
Rovers have decided they can't afford Edwards' wages, but he is determined to see out his contact and on this form deserves to be there regularly.
Rovers squandered several chances, giving Chester the confidence to stoke up their game around Derek Asamoah, on loan from Lincoln.
He was denied several times by home keeper Scott Shearer, before Rovers scored their second just before the break with Craig Disley angling a pass from Agogo well out of Gillet's reach.
Chester had left Davies, Rovers' tormentor in September, on the bench while manager Keith Curle had a look at another of his loan signings, Wayne Corden from Scunthorpe.
Davies was back on the left side of midfield to spark Chester's second-half revival and deserved his goal in the 88th minute, following a free-kick.