City pushed Stockport County all the way in an entertaining match at Edgeley Park, but could not hold on for a point against the automatic promotion challengers.
Ben House and Erik Ring struck in the first half for the Imps, but the home side - who knew only a victory would keep their hopes of finishing in second alive - threw everything at the second-half and forced their way to victory.
Paudie O’Connor returned to the starting XI, replacing Tom Hamer who dropped out of the matchday squad due to a hip injury,
That was the only change made from the team that impressed in the 4-2 win over Bolton Wanderers on Easter Monday.
Tom Hamer dropped out of the matchday squad due to a hip injury, though it is not expected to keep him out beyond this weekend.
The Imps started well and were the first side to threaten, with House getting on the end of a Reeco Hackett cross from the right. His headed effort was just wide at the near post.
And Ethan Hamilton - enjoying a fine run of form to close out the season - went on two impressive runs inside the opening 10 minutes. The first saw him skip past three players and resulted in a shot from outside the area which home keeper Corey Addai did well to held, while he was squeezed out the second time.
The home side, unbeaten at Edgeley Park since early January, were full of confidence though and had a real attacking intent as they sought to keep themselves in contention for automatic promotion.
Kyle Wootton flashed a couple of headers wide, as did Fraser Horsfall after winning the ball from a corner. Ibou Touray also saw a deflected shot bounce around the area before going just wide.
City weathered the storm and threatened on the counter. A great move from Ethan Hamilton and James Collins led to the latter winning a corner after 21 minutes - Hackett's delivery needed to be scrambled away by Addai in the home goal.
And three minutes later the Imps went ahead. Tendayi Darikwa's pass found House's run, which was timed to perfection. City' No.18 collected the ball and calmly finished past Addai's near post.
Both sides were continuing to attack, with Collins getting a shot on target after 36 minutes although there was not the power to test Addai.
But Addai was beaten again after 43 minutes, and it was a great move. O'Connor's pass was flicked on by House for Ring.
The Swede was only just inside the opposition's half when he collected the ball, but he marauded down the wing. Collins was up with him ready for a cross, but Ring finished smartly at the near post.
The home side needed to change something, and Dave Challinor made three alterations at the break - sending on Tanto Olaofe, Jayden Fevrier and Ryan Rydel in an attacking move.
And it paid dividends for the Hatters just three minutes after the restart when Fevrier's shot found its way past George Wickens, though he was aided by a deflection.
City wanted to attack and threatened, but the home side were throwing everything at the Imps backline. It was about mental fortitude now for the travelling defence.
Wootton's header across goal bounced off the inside of a post, but Jackson and O'Connor stood strong as they led the defence. The home side were largely limited to shots from distance, with Norwood firing wide after 67 minutes.
Tom Bayliss, who had replaced Ring after 62 minutes, threatened to take the ball past on the counter but was squeezed out as he tried to get his shot away.
It was Skubala's turn to make a treble change with 20 minutes to go - sending on Jack Moylan, Freddie Draper and Conor McGrandles as he wanted fresh legs on the pitch to try and see the game out.
Wickens did brilliantly to get down low to turn away a Wootton shot from distance after 75 minutes. Brad Hills rattled the crossbar from the resulting corner.
The home side's pressure saw them draw level through Will Collar after 79 minutes. He headed home Fevrier's cross from the right - leaving Wickens with no chance.
And Olaofe turned the ball home from close range moments later to put the home side ahead.
Skubala then made his final change - which was being readied before the home side went ahead - as Joe Gardner was sent on to replace Ethan Hamilton.
The goal was a real blow but the visitors pushed the home side back as they tried to find an equaliser. Moylan went close with an effort which clipped a post and bounced to safety after 88 minutes.
Imps: Wickens, Darikwa, Jackson, Erhahon, Hackett, Hamilton, Ring (Bayliss, 62), O’Connor (c), House, Roughan, Collins. Subs: Jeacock, Montsma, McGrandles, Moylan, Gardner, Draper.
Stockport County: Addai, Knoyle (Connolly, 67), Touray (Rydel, 45), Horsfall (c) (Fevrier, 45), Collar, Pye, Wootton, Moxon, Andresson (Olaofe, 45), Norwood, Hills. Subs: Wogan, Cosgrove, Bailey.
Referee: Farai Hallam.
Attendance: 9,717 (1,156 away)
