Gills took an early lead at MEMS Priestfield Stadium but were undone by two second half goals from the visitors.
Gillingham manager Peter Taylor was forced to make one change from the side that earned a superb 2-1 win at Tranmere on Friday night, Charlie Lee coming in for Myles Weston, who picked up a hamstring strain at Prenton Park.
The Gills made a fantastic start to the fixture with Cody McDonald heading onto Jake Larkins’ right hand upright inside 90 seconds, and from the resulting corner the Gills took the lead. Jake Hessenthaler delivered a high ball from the left corner flag and Bayo Akinfenwa rose unchallenged to head over the keeper and into the far corner for 1-0.
Five minutes later the home side went close again as Hessenthaler began and ended a quick counter attack. Jake sent Michael Harriman away down the right flank with a perfectly weighted pass, the ball was put out for a quickly taken throw-on, Harriman showing sharp thinking to find Cody McDonald, who laid off for Hessenthaler to shoot a low angled effort across goal that Larkins got down well to smother.
On 13 minutes Bradley Dack was unlucky to find his way into the book for a high boot challenge on Scott Cuthbert, and the O’s were unlucky not to equalise from the free-kick, Dean Cox floating a ball to the far post to meet the run of Kevin Lisbie, but the former Gills striker headed wide of Nelson’s near post.
Gillingham continued to attack with pace and move the ball around well but the O’s settled into their stride as the half wore on, going close again in the 22nd minute Moses Odubajo with a ball to the near post that Shaun Batt nodded across the Gills area, Lisbie glancing a headed finish into the hands of Stuart Nelson.
In the 28th minute Bayo Akinfinwa became the second Gillingham player to be booked for a challenge on Marvin Bartley. From the restart Orient were given a route back into the game as Leon Legge clipped Lisbie in the box, the referee pointing straight to the spot. Elliott Omozusi stepped up, only to see Stuart Nelson dive low to his right to keep out the spot-kick, the Gills defence then scrambling the loose ball to safety.
Cody McDonald went close soon after with a blocked shot that came off Omozusi before the visitors were forced to make a change when Batt pulled up injured, to be replaced by Robbie Simpson. Second after the switch Gills were denied against as Bayo headed Hessenthaler’s corner goalwards, McDonald attempted to force it home but his effort was blocked on the line.
Gillingham continued to look dangerous after the restart, Akinfenwa heading just over in the opening minute from a Nelson long ball before McDonald cut into the keeper’s near post but rolled his finish just wide of Larkins back stick.
On 54 minutes former Gills loanee Romain Vincelot appeared to be pulled back by Bradley Dack in the Gillingham half, the referee reached for a card and booked the Frenchman for simulation. As a precaution Peter Taylor opted to take the youngster off, bringing on Craig Fagan for the final 35 minutes.
Orient enjoyed plenty of possession without seriously stretching the home defence, a blocked Odubajo shot their only effort of note before Taylor made his second change just after the hour mark, Antonio German adding fresh legs to the Gills attack, in place of the goalscorer Bayo Akinfenwa.
The visitors find a route back into the game in the 70th minute with a ruthlessly effective corner routine. Dean Cox delivered a ball to meet the run of Marvin Bartley into the area, the latter plating a bullet header into the roof of the net to level the score.
In the 78th minute, Nelson was called into action to push away a curling Cox shot to his far corner, then pulled off a double save to deny Lisbie before Peter Taylor made his final change of the afternoon, introducing Danny Kedwell for Cody McDonald.
Three minutes from time substitute Yohann Lasimant found space on the right of goal to shoot for the far corner, he beat the Gills custodian but Leon Legge was well place to clear off the line as both teams looked to claim the points.
And it was the visitors that got the break-through in the final minute of normal time, Nelson coming to claim a high ball into the box, it was cleared off the line by Harriman but Lasimant was on hand at the far post to head home from close range.
Attendance: 8,613 (800 Leyton Orient)
Gillingham: Stuart Nelson, Joe Martin, Leon Legge, Bayo Akinfenwa (Antonio German 62), Cody McDonald (Danny Kedwell 81), Steven Gregory, Bradley Dack (Craig Fagan 55), Charlie Lee, Michael Harriman, Adam Barrett, Jake Hessenthaler.
Subs not used: George Howard, Callum Davies, Charlie Allen, Donervon Daniels.
Leyton Orient: Jake Larkins, Elliott Omozusi, Romain Vincelot, Scott Cuthbert (Gary Sawyer 71), Mathieu Baudry, Dean Cox, Kevin Lisbie (Yohann Lasimant 86), Moses Odubajo, Shaun Batt (Robbie Simpson 41), Nathan Clarke, Marvin Bartley
Subs not used: Harry Lee, Johnny Gorman, Sam Ling, Charlie Grainger