Jack Moylan marked his first start of the season with the decisive goal as City claimed victory at Stevenage to extend their good start to the campaign.
Head coach Michael Skubala made one change, with Moylan replacing the injured Conor McGrandles. Bailey Cadamarteri, signed on loan from Sheffield Wednesday during the week, also came onto the bench.
And it was the perfect return for the Irish midfielder, whose calm penalty conversion secured all three points at the Lamex Stadium.
It was an even opening, with Dan Kemp sending a half-volley over for the hosts with five minutes on the clock in what was the only clear opening of the first period.
City enjoyed some good possession, with a number of passes threatening to send a forward through on goal - with Ben House almost getting on the end of a Moylan pass on three separate occasions.
An Imps opportunity came from a Sean Roughan free-kick after 24 minutes. The Irishman, marking his 100th competitive appearance for the Imps, sent in a deep delivery from the right which was headed back into the area by Paudie O'Connor - with only a last-ditch header denying Adam Jackson a chance to head home his third goal of the season.
Tyreece Simpson went close to putting the home side ahead after 34 minutes after getting through on goal. George Wickens got a hand to the ball to send the Boro forward wide, and the home man could not recover and sent his effort wide.
And moments later Jovon Makama broke through at the other end. Home goalkeeper Murphy Cooper stood tall to block his efforts to lift the ball over him, but in the end referee David Rock pulled the play back having deemed Makama to have fouled Dan Butler in the build-up.
The final clear chance of the half went the way of the visitors with Makama getting away down the left. His cross nearly found House, with again a vital interception denying the Imps man a goalscoring opportunity.
Roughan went close with a low free-kick which went just wide early in the second period, as both sides worked hard to create chances.
Freddie Draper, JJ McKiernan and Cadamarteri were all sent on as the Imps tried to push the game.
And that paid dividends when McKiernan was clipped as he progressed in the area, with referee Rock immediately pointing to the spot.
Moylan stepped up to calmly slot him the 72nd-minute spot-kick, with a cool low finish into the bottom right corner.
O'Connor sent a header wide from a deep free-kick moments later as City looked to extend their lead.
The home side did enjoy plenty of the ball in the final stages as they looked to rescue a point, with Wickens standing up to Ken Aboh's header.
City were reduced to 10 men deep in time added on when O'Connor was shown a second yellow card.
Imps: George Wickens, Tendayi Darikwa, Adam Jackson, Paudie O'Connor, Sean Roughan, Dom Jefferies (Tom Hamer, 80), Ethan Erhahon, Tom Bayliss (JJ McKiernan, 59, Jack Moylan, Jovon Makama (Freddie Draper, 58), Ben House (Bailey Cadamarteri, 69). Subs not used: Zach Jeacock, Dylan Duffy, Rob Street.
Stevenage: Murphy Cooper, Dan Butler, Carl Piergianni, Dan Sweeney (Charlie Goode 19), Dan Kemp, Jordan Roberts, Tyreece Simpson (Ken Aboh, 69), Kane Smith, Elliott List (Harvey White, 70), Dan Phillips (Nick Freeman, 78), Louis Thompson (Eli King, 78. Subs not used: Dean Bouzanis, Lewis Freestone.
Referee: David Rock
Attendance: 4,017 (826 away)
