Nat Brown returned from injury to take Scott Garner's place in the centre of defence and Adam Smith replaced Jake Jones on the left as the Imps took on Nuneaton Town in a proverbial 'six-pointer' at the Triton Showers Community Arena.
City got things underway and were the first to press with Craig Hobson finding Jamie Taylor on the right but his early cross was claimed by Lee Burge. Nuneaton's response saw Danny Sleath win a corner off Brown; the flag-kick was hurriedly cleared before a dipping Aaron Phillips cross landed on the roof of Paul Farman's net.
In the 11th minute Andrew Boyce was forced to head another Phillips centre behind with skipper Alan Power well positioned to clear when the ball was played into the box. Wesley York then headed well wide after Brown deflected a cross on to the onrushing Town man.
The hosts remained on the offensive with a foul by Power on Sleath giving Town the chance to create something from a set-piece in a dangerous position but James Armson drilled well over the top. At the other end an Adam Smith cross was claimed at the second attempt under pressure from Hobson who was starting to get more involved as the half reached its midway point.
A late challenge from behind on Hobson earned Simon Forsdick a 23rd minute yellow card with the free-kick leading to the Imps' first corner which proved unproductive. Town's response saw York advance forward before Boyce got in a timely block.
On the half-hour mark the overlapping Tom Miller won another corner which was taken by Power and headed a foot over by Tony Diagne. Nuneaton's reply saw Sleath miskick as a ball was played across to him by Forsdick who had got the better of Boyce.
A quiet and scrappy period followed before the home side won another corner a couple of minutes before the break; this ending up with an attacking header looping a foot wide.
The half ended after a minute of additional play with Hobson seeing yellow for persistent infringement before referee Chris Kavanagh blew for the break.
HT: Nuneaton 0 Imps 0
Both teams emerged unchanged for the start of the second half and the Imps were the first to press with a Diagne cross landing on the top of Burge's net before Miller headed a free-kick well wide as dark clouds gathered.
At the other end a deflected Forsdick effort clipped Brown and out for a corner which was played straight out of play before the heavens opened with heavy rain falling on proceedings.
A mistimed challenge on Louis Moult earned Miller a 54th minute caution and when City responded Taylor headed a Jordan cross across the face of goal with Burge clearing with his legs. Smith then fizzed a 25-yard effort over the bar as the Imps started to turn the screw.
The strong wind and heavy rain was certainly starting to play its part with a number of forward passes out of the City defence bouncing and skidding straight out of play.
The first change of the game went Nuneaton's way in the 73rd minute with James Dance replacing Simon Forsdick whilst a couple of minutes later Jake Sheridan and Jake Jones replaced Jamie Taylor and Adam Smith for the Imps.
Sheridan was quickly in the action, skipping past his marker before sending in a cross which was cleared to Power who saw his shot blocked. Sheridan then won the first City corner of the half which saw Brown flick a header off target.
A knock to Steve O'Halloran brought about a brief break in play before a rare Town attack forced Miller to concede a corner which led to another on the opposite side. This was headed clear by Power.
Neil Cartwright repaced Louis Moult as the game entered its final three minutes with City winning another corner from their next foray forward. This came to nothing before play switched to the other end with Jordan denying Sleath a sight of goal.
Three added minutes was indicated by the Fourth Official and it appeared that these would peter out to a stalemate but this changed with just 30 seconds on the clock when, after Boyce failed to get anough purchase on a clearing header, Wesley York took a touch before rifling in a superb 25-yard effort which flew past Paul Farman for a dramatic winner.
FT: Nuneaton 1 Imps 0
City: Paul Farman, Tom Miller, Andrew Boyce, Nat Brown, Tony Diagne, Todd Jordan, Mamadou Fofana, Adam Smith, Alan Power, Jamie Taylor, Craig Hobson.
subs: Jake Sheridan (for Taylor 76), Dan Gray, Jake Jones (for Adam Smith 76), Gomez Dali, David Preece.
bookings: Hobson (45+1), Miller (54)
Nuneaton: Lee Burge, Aaron Phillips, Steve O'Halloran, Gavin Cowan, Gareth Dean, Simon Forsdick, Wesley York, James Armson, Andy Brown, Louis Moult, Danny Sleath.
subs: Neil Cartwright (for Moult 87), Jon Adams, James Dance (for Forsdick 73), Delroy Gordon, David McNamee.
goals: York (90+3)
bookings: Forsdick (23)
Referee: Chris Kavanagh
Assistants: Barry Lamb & Tom Bramall
Fourth Official: Lee Forrester
Attendance: 1,122 (324 City supporters)