Michael Skubala’s time as head coach of City got up and running thanks to Ethan Hamilton’s smart late finish at Brisbane Road.
The midfielder slotted home smartly in the 89th minute, creating space for himself before scoring into the bottom right corner.
His third league goal of the season capped an impressive second half for City, who had taken control of the game after an even opening half.
City head coach Skubala made two changes from Saturday’s game at Stevenage, with Dylan Duffy and Hakeeb Adelakun coming into the starting XI. There was also place for Gbolahan Okewoye and Charlie Parks on the bench, fresh from their starring roles in the U18 side’s 5-0 FA Youth Cup win over Walsall the previous night.
The match was preceded by an impeccably observed minute’s silence for Orient supporter Derek Reynolds, who passed away during the original playing of this fixture in October. City also paid their respects by leaving a rose on his sear before the match.
Once play got underway it was the home goalkeeper Sol Brynn who was the first called into action, with Ethan Hamilton driving a shot from distance with just five minutes on the clock. Brynn got down well to palm the effort away.
Lukas Jensen did well three minutes later after coming rushing off his line to deny first Brandon Cooper then Aaron Drinan. Joe Pigott also lifted a header over the bar for the home side.
Jack Vale twice caused consternation by closing down home goalkeeper Brynn when he had the ball - going very close to nicking the ball off him just after the hour mark before losing his footing.
The home side showed plenty of attacking intent but were largely limited to long-range shots which were no trouble for Jensen - holding Tom James’ free-kick from just outside the area as well as Idris El Mizouni’s effort.
Alex Mitchell went close to scoring against his former side just before the interval, getting on the end of Hakeeb Adelakun’s corner at the near post but flicking his effort just wide.
There were no changes from either side at the break, and City enjoyed more of the ball early after the restart.
Dylan Duffy fired an effort wide after 51 minutes, while a cross from Ali Smith just didn’t fall for Adelakun.
Adelakun tried his luck with a long-range free-kick. His powerful effort hit the wall, totally poleaxing a home defender.
Lasse Sorensen went close with a left-footed shot just before the hour mark, but his effort was blocked.
Danny Mandroiu and Jack Burroughs were sent on by Skubala after 61 minutes, replacing Adelakun and Duffy in his first changes of the game.
Mandroiu was quickly in the action, with a snapshot which was well held by Brynn.
When the home side did manage to get a shot away in the second period, Jensen was up to it with a stunning flying save to tip substitute Ethan Galbraith’s powerful effort behind. He also spread himself brilliantly to deny Ruel Sotiriou in the closing stages.
Jovon Makama, off the bench for the closing stages, almost nicked all three points for the Imps as he shugged off his man and closed on goal - pulling his low shot just wide of the far post after beating Brynn.
Then, when the chance came, Hamilton was clinical to ensure City returned north with all three points.
Orient: Brynn, James, Sweeney (Turns, 74), Happe, Pigott, (Sanders, 64), Sotiriou, Cooper. El Mizouni, Drinan (Forde,m 71), Pratley (c) (Galbraith, 74), Hunt. Subs not used: Howes (gk), Moncur, Pegrum.
Imps: Jensen, Sorensen, Jackson (c), Eyoma, Duffy (Burroughs, 61), Hamilton, Erhahon, Smith, Adelakun (Mandroiu, 61), Vale (Makama, 70) . Subs not used: Wright, Parks, Okewoye, Shodipo
Referee: Sam Allison
Attendance: 7,036 (362 away).