The Imps' unbeaten start to the Sky Bet League One season was ended by Antoni Sarcevic's strike.
The Bolton captain struck in the second period to claim all three points, and the visitors defended doggedly to defend their lead.
The Imps fans were in good voice from the off, buoyed by the pre-match confirmation of the permanent signing of TJ Eyoma from Tottenham Hotspur.
Bolton's Joel Dixon was the first keeper called into action to stop Conor McGrandles' volleyed effort from a Hakeeb Adelakun cross.
Adelakun was involved in plenty of good play from the Imps in the opening period, playing the ball across to Regan Poole who sent a first-time strike just over the bar.
Adelakun himself saw an effort blocked, after collecting the ball from Edun.
Lasse Sorensen pinged a low shot just wide as the half drew to a close after Edun's cross, flicked on by Tom Hopper, was cleared.
The first chance of the second period fell to Scully, who cut inside from the left before unleashing a curling effort which went just wide of the far post.
Dapo Afolayan and Eoin Doyle went close to forcing the ball home for Wanderers before it was cleared by the Imps.
The busy Adelakun ran into area and held off several defenders before laying the ball off for Sorensen but his shot lacked enough power to trouble Dixon.
The visitors went ahead after 77 minutes when Afolayan's shot was blocked and
Antoni Sarcevic followed up to blast home.
Dan Nlundulu and Lewis Fiorini were sent on as the Imps pushed to equalise, but the visitors defended in numbers.
Cohen Bramall's free-kick from distance provided the best opportunity for the home side, but it was deflected and Dixon collected.
