Bohan Dixon replaced the suspended Alan Power for this FA Carlsberg Trophy Second Round tie at Braintree Town whilst scholar Callum Ward was named on the bench for the first time.
City kicked off in front of a very sparse crowd and were quickly on the offensive with Sean Newton getting the better of his markers down the left before whipping in a cross which found fellow full-back Tom Miller who blazed over.
Braintree's response saw Kenny Davis latch on to a back-heel after Jake Sheridan had conceded possession before testing Paul Farman with a low drive. At the other end Todd Jordan set his sights from long range but drilled well over.
A quiet spell ensued before the first corner of the game on the quarter-hour mark ended up with Jordan sending an overhead kick just wide.
Six minutes later the deadlock was broken with a goal out of nothing; a free-kick from deep after Dixon was harshly penalised for a foul on Dean Wells wasn't dealt with and on hand to smash home was Sean Marks who gave Paul Farman no chance from 12 yards.
Shortly after the restart a City free-kick gave Newton the chance to set his sights but his effort clipped the wall for a corner. Another flag-kick quickly followed and when this was played back to taker Newton, his excellent centre was headed home by Chris Sharp only for his effort to be ruled out for offside.
A knock to scorer Marks brought about a lengthy break in play as the half-hour mark approached and when play restarted Newton tested Nik Hamann from range after the Imps pushed forward again.
Ten minutes before the break a rare Braintree attack ended up with Dan Holman winning a corner which was easily dealt with before another scrappy period of play came along with a number of free-kicks doing nothing to aid the flow of the game.
The last half-chance of the opening 45 minutes saw home stopper Hamann claim a deflected Sheridan effort after a long Miller throw fell to him 25 yards out.
The half ended after three added minutes, during which Dixon was booked for a stray arm on his marker.
HT: Braintree 1 Imps 0
Both teams emerged unchanged for the start of the second half and it was the hosts who were the quickest out of the traps, winning a corner a couple of minutes in which was headed well over Matt Paine at the back post.
A blatant block on Sheridan earned Davis a yellow card five minutes in and as the Imps pushed for a leveller early on a couple of long Miller throws failed to come up trumps.
It wasn't long before the Imps were pushing forward again though and in the 58th minute Newton picked out CHRIS SHARP and he marked the start of his second month on loan from Hereford with a neat header which fizzed past Hamann and into the top corner for a deserved leveller.
A clash of heads between Marlon Jackson and former City trialist Sam Habergham saw play come to a break just past the hour mark
When play resumed Sheridan was cautioned following an off-the-ball tussle wih Alan Massey, who seemed to escape punishment for his part in the misdemeanour.
A double change for the hosts as the game entered its final quarter saw Exodus Geohaghon and James Muley replace Chez Isaac and Dan Sparkes. A Miller throw-in then ended up with Jackson firing over from the edge of the box.
In the 77th minute Jordan saw yellow for a challenge on Mulley with the hosts sending the resultant free-kick straight out for a goal-kick. Habergham then tested Farman following a rare Braintree attack.
A third and final Town change saw Jordan Cox come on for Kenny Davis a couple of minutes later before a long Geohaghon throw was headed over by Wells from close range.
A knock to Jackson saw physio Kev Oxby stretch his legs for the first time and he was immediately replaced by Nick Wright with two minutes on the clock.
City remained on the offensive though and when the industrious Newton won a throw on the left in the last minute of normal time, Miller hurled the ball in and up rose LUKE FOSTER to flick a header into the top corner for his first of the season.
This proved to be Miller's last action of the game as he limped off shortly after the Fourth Official indicated. Danny Rowe was his replacement.
Play carried on and after the Imps withstood a long ball into the box, they attacked and when Sharp was released down the middle he was denied by Hamann. The ball was kept alive by Wright and he picked out Dixon who saw his shot hit post before crashing against Hamann and back into the net to secure the Imps' passage into the last 16 of the competition.
FT: Braintree 1 Imps 3