City suffered only their fourth league defeat of the season as they were beaten at Rotherham United.
Michael Skubala mades five changes to the side that took on Salford City in the Emirates FA Cup last weekend with Tom Hamer, Sonny Bradley, Tom Bayliss, Rob Street and Justin Obikwu all coming into the starting XI.
The opening period was end to end with the Imps forcing a couple of early corners, and they did have the ball in the back of the net in just the sixth minute but Justin Obikwu's effort was ruled out for offside.
And the bright start continued after Adam Reach won the ball back well out on the left and fed Freddie Draper, with the later looking to catch home keeper Cameron Dawson out.
The Imps may have narrowly edged the opening 10 minutes, but the home side struck first. Reece James collected the ball from Dan Gore before lining up a long-range shot from outside the area which beat George Wickens after a high bounce off the pitch just in front of him.
Sonny Bradley headed over from a right-wing cross as City looked to respond quickly and, with 15 minutes on the clock, Erik Ring's ball looking for the run of Obikwu was just too far ahead of him.
Obikwu won the ball back on the right and looked to pull the ball back for a team-mate, with Hamish Douglas on hand for a vital clearance. Draper was also squeezed out by a combination of three Millers defenders in the area as he tried to fashion a shooting opportunity.
The home side doubled their lead just after the half hour mark. A well-worked corner from Joe Powell created space for Ar'Jany Martha who powered home from outside the area.
City did not give up hope of getting a goal back before the break, with Street getting on the end of a Ring free-kick - the referee's whistle had already gone before Street connected with the header.
A Hamer throw from the right was flicked on by Street, with Draper just struggling to get his leg high enough to get over his volleyed shot at the far post and had to watch as the ball went agonisingly wide of a post.
Wickens had to be alert to scramble over to tip away an effort from Sam Nombe, after Jordan Hugill's header down from a quick counter-attack.
And a couple of minutes into time added, at the other end of the pitch, Dawson pulled off a great save with his legs after Street's driven close-range effort after Obikwu headed the ball on.
There were no changes from either side at the break, and the Imps again started with purpose - with a Conor McGrandles ball just ahead of Street's run.
Ring's cross, looking for Obikwu and Street, was deflected behind for corner from which Jackson headed just over after doing well to win the ball. The assistant's flag was up again to stop Obikwu after Jackson's clipped clearance looking for him.
For all that pressure, the home side effectively sealed the game on the hour mark when a clearance from the left found Denzel Hall whose powerful effort found the bottom far corner.
Skubala made three changes to look to change the match with Ivan Varfolomeev, James Collins and Oscar Thorn all sent on.
Varfolomeev almost opened his goalscoring account for the club a few minutes after his arrival as he headed the ball past Dawson, with James getting back to clear. When the ball found its way back into the area Jackson won the header but could not direct it towards goal.
There was a good move as Thorn combined with Street down the right, but the substitute pulled his effort wide. Again the Imps got the ball back into the area quickly, with Hamer's header going agonisingly over the bar.
And Street flashed an header just over from a Dexter Lembikisa cross from the left on a day where it just didn't work out for the Imps.
Rotherham United: Dawson, Rafferty, James, Powell, Hugill (Sherif 80’), Nombe (Benson 88’), Martha (Kaleta 93’), McWilliams (Yearwood 80), Hall, Douglas, Gore. Unused subs: Cann, Ayres, Holmes
Imps: Wickens, Reach (Lembikisa, 79), Jackson, Bayliss, Ring (Okoronkwo, 69), McGrandles (Varfolomeev 63), Bradley, Street, Obikwu (Thorn, 63), Hamer, Draper (Collins, 63). Subs: Jeacock, Towler
Attendance: 8,912 (1,534 away)