Ollie Watkins got the only goal of the night for Exeter in the first half with a close range strike to take them off the bottom of the table, as Orient flirt just above the relegation zone.
Alberto Cavasin made two changes to his side that lost 2-1 at home to Blackpool, as Myles Judd got his first league start for the club with Yvan Erichot out injured. Paul McCallum’s late impact on Saturday earned his call up to the starting eleven, ahead of Ollie Palmer who moved to the bench.
Exeter took the lead 25 minutes in, on the break as Liam McAlinden long deep cross found David Wheeler, who put the ball across goal for Watkins to slot into the far corner.
Orient almost struck straight back, after a sloppy back pass by Exeter played Jay Simpson in down the left flank but held the ball up, as Christy Pym rushed out and the opportunity closed with his pass going astray and was cleared.
Gavin Massey was brought down just outside the box, as Nicky Hunt stepped up and fired the set piece just over the bar.
Exeter thought they had grabbed a second, as McAlinden whipped in a ball on a plate for Watkins unmarked inside the box but his header went wide from six-yards out – despite the offside flag.
Orient’s Alex Cisak came to collect a high ball which he miss-timed, with Wheeler waiting to poach he lifted the ball across the box which was half cleared by Hunt and the danger eventually cleared.
In added time of the first half, Michael Collins burst into box for the O’s and cut across a teasing ball but Exeter Captain Jordan Moore-Taylor did enough flick it away for a corner.
Exeter nearly extended their advantage, as Watkins was in space just inside the box and slotted it into McAlinden who turned his shot goal wards but was saved at the feet of Cisak.
Orient should have equalised 67 minutes in, as Massey’s low ball across goal was slotted towards goal by Nigel Atangana but stopped by Pym. Atangana got to the second ball and his shot rebounded back off the defender and fell to Simpson from close range whose shot was blocked and went over the bar.
Leyton Orient Lineup: 1 Alex Cisak, 16 Nicky Hunt, 29 Myles Judd, 6 Tom Parkes, 3 Callum Kennedy (45), 11 Gavin Massey, 8 Robbie Weir © (45), 15 Nigel Atangana, 7 Michael Collins, 10 Paul McCallum (59), 27 Jay Simpson
Substitutes: 24 Sam Sargeant, 25 Aron Pollock, 5 Alan Dunne (45), 32 Henry Ochieng, 22 Sandro Semedo (45), 30 Sam Dalby, 9 Ollie Palmer
Exeter City Lineup: 30 Christy Pym, 3 Craig Woodman, 4 Lloyd James, 11 David Wheeler (66), 14 Ollie Watkins (88), 15 Jordan Moore-Taylor ©, 19 Liam McAlinden, 25 Jake Taylor, 29 Luke Croll, 31 Pierce Sweeney, 33 Reuben Reid (66)
Substitutes: 1 Bobby Olejnik, 8 Robbie Simpson (88), 12 Joel Grant, 16 Matt Oakley (65), 28 Jack Stacey (66), 39 Troy Brown, 20 Matt Jay