The Imps never got going throughout the 90 minutes and having trailed to a fifth minute Kevin Betsy penalty after Jake Sheridan was penalised for a trip in the area, it was always going to be an uphill battle.
That battle was eventually won by the visitors when striker Bradley Bubb was set free down the middle with his neat finish earning his side the three points.
There were three changes to the side that started Saturday's FA Cup with Budweiser Second Round tie against Mansfield Town for this Blue Square Bet Premier clash against Woking at The 12th Imp Sincil Bank Stadium with Tom Miller, Mo Fofana and Adam Smith being replaced by Scott Garner, David Morgan and Aristide Bassele. Whilst Miller and Fofana were rested completely, Smith was on the bench where he was joined by new signing, goalkeeper David Preece.
Early evening rain made for a greasy surface as referee Chris Kavanagh led the two teams out of the tunnel and once play commenced City enjoyed the better of the early exchanges but with just five minutes on the clock, Woking's first attack led to them taking the lead when Jake Sheridan was harshly penalised for a foul on Brett Williams.
Sheridan's appeals that he won the ball and conceded a corner fell on deaf ears, though, with referee Kavanagh awarding the visitors a penalty. The experienced Kevin Betsy duly sent Paul Farman the wrong way from the spot.
City looked for a quick response with Bassele sprinting down the left before seeing his final touch go through to Woking 'keeper Aaron Howe whilst shortly afterwards skipper Gary Mills was pulled up for handball as he tried to keep a long Dan Gray throw-in in play.
In the 11th minute Jamie Taylor came close to connecting with a Sheridan pass and as City pushed forward again Sheridan was upended for a free-kick in a decent position. This ended with Howe punching away Morgan's centre before Sheridan fired over.
The Imps continued on the offensive with a neat flick from Power releasing Morgan whose touch past the advancing Howe saw the ball go out with the 'keeper fortunate not to trip the City midfielder as he burst into the box.
As the half approached its midway point, City 'keeper Farman needed attention to his left eye and when play restarted Taylor had a shot easily gathered by Howe. At the other end Farman was forced to go down and claim a low Billy Knott drive.
A clever Taylor pass then found Mills who saw his ball across to Bassele blocked and deflected out for a corner which was hurriedly cleared by the Woking defence. Andrew Boyce then had a header from a Gray cross saved as the Imps pressed forward again.
On the half-hour mark a Power shot was then deflected behind but this corner ended u with Mills conceding play cheaply and allowed Bradley Bubb to break forward before firing into the side netting.
A minute later a weak pass back to Farman by Gilbert forced the City stopper off his line before his clearance crashed against Williams and out for a goal-kick. A misunderstanding between Garner and Bassele then led to a Woking corner which was wasted by the visitors.
With heavy rain starting to fall a scrappy half continued, although a foul by Mark Ricketts on Taylor gave the Imps a free-kick on their left but again the visitors repelled the danger. At the other end Garner was forced to concede a corner which led to another on the opposite side.
Garner was booked for a clumsy challenge on Betsy just before the Fourth Official indicated that a minimum of two minutes was to be added on whilst the last action of the opening period saw a long ball from Gray flicked off Power's boot by Adam Newton for a City corner which came to nothing.
HT: Imps 0 Woking 1
Prior to the start of the second half Vadaine Oliver replaced Bassele for the Imps and he was quickly in the action winning a couple of headers whilst at the other end Farman was forced to gather a dangerous cross from left-back Mike Cester.
City started brightly with a corner three minutes in ending up with Morgan stabbing just wide and after this was cleared the Imps kept the ball in the attacking third with Oliver proving to be more than a nuisance following his arrival.
A long-range Morgan was the next effort at goal but his 25-yarder went well before a cut knee forced Garner to the sidelines for treatment just after the hour mark.
After the early pressure thing were drying up for the Imps in terms of attempts at goal, although a Taylor snap-shot was held by Rowe before an Oliver knockdown from a Gray centre just went behind Taylor.
Shortly afterwards the visitors doubled their advantage when Bubb was released through the centre and he finished neatly past the advancing Farman as the game approached its final quarter.
Imps' boss David Holdsworth responded by bringing on Colin Larkin for David Morgan before Cestor was cautioned for dragging Taylor to the deck. The resultant free-kick, taken by Power, was flicked wide by Gilbert inside the six-yard box.
A double Woking change with 15 minutes on the clock saw Jayden Stockley and Gavin McCallum replace Brett Williams and goalscorer Bubb.
City then had Farman to thank as he palmed away a goalbound Knott effort whilst at the other end the Imps' lack of luck came to the fore when Mills saw his low drive clip Oliver's heels before the ball flew out for a goal-kick.
A swift break then ended up with Power having a low drive held by Rowe whilst a change for both sides saw Adam Smith replace Jake Sherdian for the Imps and Dean Sinclair came on for Lee Sawyer for the visitors.
A superb block from Boyce denied Knott a third Woking goal and from the resultant corner ex-Imp McCallum fired wide after Farman failed to claim the centre. City's response saw Mills drag a poor effort well wide.
In the final minute of normal time Mills was picked out by Gray only to head over the bar whilst in the second of four added minutes Taylor was booked for knocking the ball out of Rowe's hands as he prepared to drop kick the ball forward.
FT: Imps 0 Woking 2
City: Paul Farman, Dan Gray, Andrew Boyce, Scott Garner, Peter Gilbert, Gary Mills, David Morgan, Jake Sheridan, Aristide Bassele, Alan Power, Jamie Taylor.
subs: Adam Smith (for Sheridan 84), Vadaine Oliver (for Bassele h/t), Peter Bore, Colin Larkin (for Morgan 70), David Preece.
bookings: Garner (45), Taylor (90+2)
Woking: Aaron Howe, Adam Newton, Joe Mcnerney, Adam Doyle, Mike Cestor, Mark Ricketts, Lee Sawyer, Kevin Betsy, Billy Knott, Brett Williams, Bradley Bubb.
subs: Loick Pires, Dean Sinclair (for Sawyer 84), Gavin McCallum (for Bubb 76), Jayden Stockley (for Williams 75), Sam Beasant.
goals: Betsy (5), Bubb (67)
bookings: Cestor (73)
Referee: Chris Kavanagh
Assistants: Andrew Tonks & Graham Kinnear
Fourth Official: Craig Grundy
Attendance: 2,562 (63 visiting supporters)