Tendayi Darikwa's goal earned the Imps victory at Northampton.
The right wing-back's first-half strike sealed a deserved three points, as Michael Skubala built on the positive aspects seen in the performances against Birmingham City and Bolton Wanderers.
Conor McGrandles and Ben House returned to the starting XI as Skubala made those two changes from the midweek Vertu Trophy game against Bolton Wanderers. Zach Jeacock kept his place in goal with George Wickens missing due to a shoulder injury.
Bailey Cadamarteri was absent after picking up an injury, with the Imps waiting for the results of a scan. He has passed the cut-off point where his parent club Sheffield Wednesday can recall him, meaning he will remain in Lincolnshire until the conclusion of the season.
It was an even opening as both sides settled into the game, with the Imps winning their first corner after six minutes through Draper after a well worked counter.
The Cobblers' greatest threat came from Mitch Pinnock's long throws, with Conor McGrandles hooking one delivery away which away supporters nervously thought might creep in at the far post (although replays made clear it would not have).
Moylan fired over after 16 minutes, as the Imps grew in confidence, and a couple of minutes later Ben House headed just over from a Jack Moylan corner.
House threatened to break through when Ethan Erhahon sent a ball into space, but Jordan Wills got across well to get a foot on the ball.
The Imps were forced into a change just before the half hour mark when Jack Moylan was injured in a challenge with Willis, with Tom Bayliss coming on in his place.
The breakthrough came after 38 minutes when Draper sent House through on goal. House, under pressure, saw his shot come off the far post. Darikwa slid the ball home despite the best efforts of Pinnock.
The Imps had their tails up and pressed for a second before the break, with Draper going close to quickly doubling the advantage.
City again started the second period brightly, with Bayliss flicking a header just wide from Sean Roughan's cross in the opening minute of the half.
The home side were also fired up, having brought on Tarique Fosu in an attacking change at the break. TJ Eyoma saw an effort roll wide as he tried to place the ball in the far corner, while Tom Eaves won a header but could only direct his effort straight into the arms of Zach Jeacock.
The Imps rode out that initial period of pressure from the Cobblers and were threatening again as the match reached the hour mark.
Nik Tsanev did well to get down and block a powerful low effort from Reeco Hackett, after Willis was unable to clear.
The Imps were resolute in defence and limited the home side's chances, with Jeaccock alert to punch away Eaves' looping half-volley after 68 minutes.
Skubala's side looked to take advantage of gaps left in the home defence and put the game to bed, with Darikwa finding House with a great diagonal ball. House controlled the ball magnificently and pulled it back looking for Draper, with only a vital clearance denying the Academy product a chance.
Jeacock was again needed to turn away a Eaves header, but City stayed strong to claim all three points.
Imps: Jeacock, Darikwa, Jackson, Erhahon, Hackett (Jefferies, 72), McGrandles, O’Connor (c), House, Roughan, Moylan (Bayliss, 28), Draper (Makama, 84). Subs: Pardington, Montsma, Hamilton, Ring.
Cobblers: Tzanev, McGowan (c)(Dyche, 90), Willis, Hoskins, Eaves, Pinnock, Odimayo, Hondermarck (Wilson, 79), Eyoma, Shaw, Chouchane (Fosu, 45). Subs: Burge, Tominson, Dobson, Obiagwu.
Attendance: 6,094 (547 away),
