City were edged out in a close affair at Rotherham United.
Jovon Makama's powerful effort early in the second half looked set to have earned the visitors a point, after Sam Nombe's opener, but Sean Raggett struck with a stunning header against his former side to claim victory.
Head coach Michael Skubala made three changes, with Ben House, Adam Jackson and Conor McGrandles returning to the starting XI. House had recovered from the illness which kept him out of Saturday's Emirates FA Cup win at Crawley Town, while Jackson returned as Lewis Montsma was rested as part of his phased return from a knee injury.
The match was delayed half an hour by a power cut in the areas surrounding the AESSEAL Stadium, and just five minutes after the kick-off the Imps were forced to change plans again as a nasty head collision between home player Hakeem Odoffin and Jackson left the latter needing to come off. Dom Jefferies was called upon, slotting in at right-back with Tendayi Darikwa moving inside.
City were able to impose themselves on the game, with House forcing a great save out of Dillon Phillips after nine minutes. Ethan Erhanon won the ball back inside the Millers' half and played House through, with the returning No.18 stinging the palms of Phillips with a rasping drive.
And the Imps threatened from the resulting corner, which saw Sean Roughan link with Jack Moylan before the latter clipped the ball across the area. Jefferies got the ball back towards the centre of goal with former Imp Sean Raggett alert to head the ball away,
Zak Jules' headed effort after 14 minutes was comfortable for George Wickens, but he was beaten seven minutes later when Sam Nombe rose highest to nod home Reece James' left-wing cross.
Moylan went close to an equaliser after 28 minutes, again after City won the ball back inside the home half. Ethan Hamilton clipped the ball over for Moylan who tried a low finish only to be blocked by Phillips' trailing leg.
A nice move saw House through on goal after 34 minutes, as he got past Raggett, but Phillips was out quickly to smother the shot.
The Imps made a second change at the interval, with Reeco Hackett coming on in place of Hamilton.
City started the second half brightly and won a free-kick in a dangerous position two minutes in after House was clipped by Zak Jules just outside the area. It proved a decisive free-kick as Moylan's powerful effort tested Phillips.
The home keeper could not hold the shot and Makama shrugged off Nombe before lashing home despite James sliding in for the home side.
House found himself in a good position moments later, but could not connect cleanly with Hackett's cross from the left. House got a shot away again, but did not have the power to test Phillips.
The home side went back ahead after 77 minutes when Raggett powered home Joe Powell's cross.
City pushed to level, with Bailey Cadamarteri almost flicking home a header from Roughan's corner.
And, as the Imps kept up the pressure, McGrandles saw an effort blocked after doing well to create space for a shot.
There was late drama as a Moylan corner led to a scramble, with neither Draper, Darikwa nor O'Connor able to get clear connections on their shots.
Ring then Cadamarteri both went close in time added on, but despite City's efforts there was no way back.
Imps: Wickens, Darikwa, Jackson (Jefferies, 7), Erhahon, Hamilton (Hackett, 45), McGrandles, House (Draper, 67), O'Connor (c), Roughan, Makama (Cadamarteri, 79), Moylan (Ring, 80).
Substitutes: Pardington, McKiernan, Jefferies.
Millers: Phillips, Rafferty, Raggett, James (McCart, 90+5), Powell, Nombe, Clarke-Harris (c) (MacDonald, 90+2), Wilks (McWilliams, 90), Jules, Odoffin, Tiemi.
Substitutes: Humphreys, Hugill, Green, Hungbo.
Official: Martin Woods
Attendance: 8,995 (1,256 away)