Andy Cook scored the winner for the Merseyside outfit despite the Seals heading in-front twice through James Alabi and Ryan Astles.
Rovers staged a second-half goal fest in-front of the BT Sport cameras with Jay Harris and James Norwood adding the first and second towards their third successive win.
The blue’s performance was worthy of taking something away from the game but instead, leaves a bitter taste.
Just two minutes in, Chester were awarded a penalty. Ritchie Sutton brought down Evan Horwood, meaning Alabi converted to make it 1-0.
After the restart, Rovers levelled the scoring through Harris who found the bottom corner on 54 minutes.
14 minutes on and the home side headed in-front courtesy of Astles, assisted froma Ryan Lloyd corner.
Blue’s news recruit Lucas Dawson came on for Kane Richards to shake things up in the midfield.
Norwood brought the game to a stalemate when Liam Ridgehalgh crossed and found the forward to nod home his 19th goal for the away side.
Rovers completed the comeback on 89 minutes when Cook’s 18-yard strike flew past Alex Lynch to send the travelling support into delirium.
Seven additional minutes were added on but the home side couldn’t find an equaliser.
Tranmere held off Chester pressure to go five matches unbeaten, whilst the Deva Stadium outfit are in 11th place losing five of the last seven games.