With the appeal against Jake Sheridan's sending off against Dartford proving unfruitful, City boss David Holdsworth was forced to make one change to his starting line-up with Jake Jones coming on for his full debut. Jones started on the left with Adam Smith switching to the opposite flank.
With a chill in the air, Stockport kicked off and were the first to press with the overlapping Sean Newton winning a corner in the second minute but the Imps' defence stood firm with play quickly switching to the other end and when Jones was pushed in the back, skipper Alan Power forced Richard O'Donnell to tip his free-kick behind at full stretch. This flag-kick ended up seeing Andrew Boyce head wide.
Smith then fed a clever ball through to Tom Miller who saw his pacy ball into the box fly past everyone whilst at the other end Mark Cullen picked out Matty Mainwaring who saw his first time effort curl well wide of David Preece's left-hand upright.
City responded with the lively Jones skipping past his marker before being denied by O'Donnell before, after a quiet spell, Vadaine Oliver had a header from a looping Power cross claimed by the County stopper.
As the half-hour approached, Oliver and Jones were denied again in quick succession after a slip from Jordan Fagbola gifted the former possession. The home fans were then quick to voice their frustration as a number of decisions went against their players; two City corners did nothing to help their mood with Boyce heading the second wide.
After the Imps defended a corner at the opposite end, Smith and Jones swapped flanks with the former latching on to an Oliver lay-off before cutting in and curling just wide from 25 yards out.
One minute of added time was indicated by the Fourth official and as this approached its conclusion, O'Donnell made a hash of a Smith cross and when the ball ran loose to Jones, he was crudely upended by the 'keeper with referee Ben Toner quick to point to the spot.
Colin Larkin, fresh from his late penalty success against Dartford on Saturday, stepped up but this time his radar went astray as he dragged his low effort wide of the target with O'Donnell flinging himself in the opposite direction. Before play restarted and the half ended, Jon Nolan was cautioned for dissent.
HT: Stockport 0 Imps 0
Both sides emerged unchanged for the start of the second half and the Imps were the first to press with O'Donnell forced to claim a Smith cross under pressure from Oliver. At the other end a Stockport attack saw Cullen fire in a shot which flew past Preece only to crash against the post and away to safety.
City dealt with a Stockport corner eight minutes in before Jones hooked away a Mainwaring cross and Power denied Nolan a sight of goal with a timely intervention on the edge of the box.
Stockport kept up the pressure and it wasn't long before they grabbed the lead with Danny Hattersley latching on to a through ball into the area and, one-on-one with Preece, he neatly slotted the ball past the City stopper from a narrowing angle.
City's response saw Olvier volley wide following a Fagbola slip whilst a few minutes later Power was harshly penalised for a foul on Mainwaring as he surged down the middle. The free-kick was taken by Newton and he duly planted his left-footed effort past the wall and Preece to double his side's advantage.
Before play restarted Conner Robinson and Jamie Taylor replaced Adam Smith and Colin Larkin but it wasn't long before the home side were on the attack with Cullen meeting a Newton cross only for Preece to palm away his header.
Home skipper James Tunnicliffe was booked for a late challenge on Taylor before Adnan Cirak replaced Hattersley up front for the Hatters. City were now up against a County side who were clearly lifted following their double strike.
Sam Sheridan for Connor Jennings was County's second change before Cullen tested Preece with a low drive. Chances at the other end remained at a premium as the game entered its final 10 minutes, although O'Donnell fumbled a Taylor effort before the impressive Jones drilled a left-footed effort over the bar from the edge of the box.
Jones was replaced by Nicky Nicolau for the last five minutes and Nicolau's first taste of the action saw him replace Power who went to ground in the box only for his appeals for a penalty to be waved away by referee Toner.
The final substitution saw Mark Cullen make way for Danny Whitehead in the final minute whilst in the first of four added minutes Power sliced wide from the edge of the box. Boyce was pushed up in a last ditch effort to salvage something from the game but the earlier damage proved to be enough and the Imps were left to reflect on a 2-0 reverse on away soil.
FT: Stockport 2 Imps 0
City: David Preece, Tom Miller, Andrew Boyce, Scott Garner, Peter Gilbert, Paul Turnbull, Alan Power, Jake Jones, Adam Smith, Vadaine Oliver, Colin Larkin.
subs: Jamie Taylor (for Larkin 64), Dan Gray, Nicky Nicolau (for Jones 86), Conner Robinson (for Smith 64), Paul Farman.
bookings: Power (62)
Stockport: Richard O'Donnell, Andy Halls, Sean Newton, James Tunnicliffe, Alex Kenyon, Danny Hattersley, Mark Cullen, Jon Nolan, Jordan Fagbola, Matt Mainwaring, Conner Jennings.
subs: Joe Connor (for Jennings 75), Danny Whitehead (for Cullen 90), Sam Sheridan, Adnan Cirak (for Hattersley 71), Ian Ormson.
goals: Hattersley (57), Newton (63)
bookings: Nolan (45+3), Tunnicliffe (70)
Referee: Ben Toner
Assistants: Ian Johnston & Alix Pashley
Fourth Official: Natalie Walker