Two set piece goals in two second half proved to be Town's undoing as Tranmere Rovers ran out 3-2 winners in an action packed evening at Prenton Park.
Josh McPake's first Town goal had given his side the lead, but James Vaughan levelled from the penalty spot before the interval.
It was early in the second half when the irreversable damage was done as both Kaiyne Woolery and Vaughan profited from slack marking to put their side 3-1 up.
With Connor Hall dismissed for a second yellow card, Town pulled one back through Josh March's header, but couldn't find an elusive equaliser in the final stages.
Simon Weaver made one change from Friday night's point at Salford as Warren Burrell returned from suspension, taking the place of Jay Williams.
Both sides showed their attacking intent from the off with Liam Feeney threatening down the left for the hosts and McPake forcing Scott Davies into an early save.
The first real chance of the evening fell to Aaron Martin after a cross from the right was helped on by Brendan Kiernan, but Town's number ten couldn't guide his header into the corner.
Town were looking the more dangerous of the sides and created another opening in the 16th minute as McPake picked out Thomson just inside Rovers' area, the midfielder's powerful drive well blocked.
A deserved breakthrough arrived in the 25th minute as Thomson spread the ball left to McPake, who drove towards goal and finished from a narrow angle.
The hosts were given the chance to reply in the 34th minute as Referee Andy Haines harshly pointed to the spot after Burrell challenged Manny Monthe.
Vaughen stepped up confidently and levelled, sending the sides into half time a;ll square, but not before a bad tempered final ten minutes of the half, with strong challenges flying in from both sides.
Tranmere took the lead six minutes into the second half when a corner was won in thew air by Peter Clarke and fell to an unmarked Kaiyne Woolery, who calmly swept into the net.
Town were undone by another corner two minutes later with the ball dropping to Vaughan on the line, perfectly placed to tap home his second of the night.
Weaver shuffled his pack on the hour mark with Simon Power and Josh March introduced, but were reduced to ten men nine minutes later as Hall was shown a second yellow card for halting a Tranmere attack, the first booking coming in the first half for protesting the Referee's penalty decision.
Despite being a man down, Town reduced the deficit to one when March claimed his first goal for the club, flicking Thomson's free kick delivery into the top corner.
A brilliant point blank James Belshaw save prevented Vaughan claiming his hattrick in the 74th minute, Town's stopper blocking the striker's diving header.
March went close to what would have been a second stoppage time equaliser in the space of five days for Town, but Davies was able to spread himself, block the strike and secure three points for Rovers.
Town: Belshaw, Falkingham, Burrell, Thomson, Martin, Lawlor, Kiernan (Power 60), Muldoon (March 60), Hall, Francis, McPake
Subs not used: Hondermarck, Kirby, Minter, Williams
Goals: McPake 25, March 72
Sent off: Hall
Tranmere Rovers: Davies, Monthe, Spearing, Vaughan (Ray 93), Woolery (Morris 72), Khan, Macdonald, Feeney (Ferrier 93), Lewis, Clarke, Lloyd (Ridehalgh 73)
Subs not used: Murphy, O'Connor, Kirby
Goals: Vaughan 36(p), 53, Woolery 51
Booked: Macdonald, Lewis, Vaughan
Referee: A Haines