BIRKENHEAD-BORN Ryan Astles grabbed Chester a share of the spoils in stoppage time.
Astles connected with a Johnny Hunt cross and saw his low strike find the bottom left corner of thed net.
Chester made just one change from the side that had suffered a 5-2 home loss against Lincoln City.
Striker Kane Richards started in place of Jordan Chapell.
Two goals in a four-minute spell put Tranmere in control before the break.
Andy Cook's 20-yard half volley after controlling a right wing cross from Ben Tollitt broke the deadlock in the 30th minute.
And Tollitt scored a controversial goal four minutes later when he looked like he had handled before netting an 18 yard shot.
Chester provided a good response, but Richards hit the bar with a 12 yard shot after receiving an assist from Craig Mahon.
Elliott Durrell then turned his marker on the edge of the penalty box but saw his low strike easily claimed by home keeper Scott Davies.
Chester made a perfect start to the second half as they reduced their arrears.
Tom Shaw produced a perfect headed goal after meeting a delivery from Ryan Lloyd in the 50th minute.
And Shaw was presented with another scoring chance minutes later when he was offered a free header from a Durrell cross but saw his effort saved by Davies.
Blues keeper Alex Lynch made a great save to deny Andy Mangan from close range minutes later as Tranmere attempted to steady the ship.
Rovers were reduced to 10 men in the 65th minute when Tollitt received a second booking for diving.
Durrell fired wide from 25 yards before Ryan Astles headed wide at the near post from a Durrell corner as Chester pressed.
And Lloyd rifled a 15 yard shot over the bar after good work from Mahon.
Ryan Astles levelled matters in the third minute of injury time when he met a cross frtom Johnny Hunt and saw his first time low shot find the bottom left corner of the net.
TRANMERE ROVERS (4-4-2): Davies; Vaughan, Ridehalgh, McNulty, Harris, Cook, Sutton, Kirby (Mekki 83), Tollitt, Mangan (Ihiekwe 68), Hughes. Subs (not used): Turner, Stephenson, Dawson.
CHESTER (4-4-2): Lynch; Hughes, Astles, Hudson, Hunt; Shaw, Lloyd, Durrell, Mahon; Richards, Alabi. Subs (not used): Evans, Marsh, Joyce, Chapell, Horwood.
REFEREE: Thomas Bramall (Sheffield).
ATTENDANCE: 7,790 (1,129 from Chester).
Full report and pictures in Mondays' Leader.