npower League 1
The next opening resulted in a lengthy stoppage as Charlie MacDonald caught goalkeeper Bartosz Bialkowski in the head as the keeper dived in to collect a through ball.
MacDonald received a yellow card for the challenge, while the Magpies stopper wasn't fit to continue and sub Fabian Speiss entered in his place.
Lee Cook was looking like Orient's most likely provider and he warmed Speiss' palms with a stinging drive from the edge of the box on the half hour.
The half chances were falling the O's way and Speiss had to claw the ball off MacDonald's toes in first half stoppage time after Cook knocked the ball back into the middle and Mooney couldn't make contact.
Notts County's best chances also arrived in the eight minutes of added time, as Yoann Arquin sent a header against the crossbar following an Alan Sheehan cross, then Lloyd James had to clear off the line to deny Enoch Showunmi after Jamie Jones failed to reach a corner.
The Magpies also got off on the front foot at the start of the second period, with Jamal Campbell-Ryce making a threatening run down the right before standing up a cross which Showunmi headed over the top.
Orient won a free kick at the other end on 56 minutes and were so close to taking the lead as Martin Rowlands' effort deflected off the wall and fell for Mathieu Baudry to guide goalwards, but Speiss got down brilliantly to tip the ball around the post.
The German stopper was involved again two minutes later, closing down the angles to save from Mooney after Cook had played him in.
County couldn't hold out for much longer though and Orient went in front on 65 minutes when Cook's thunderous drive was only touched onto the crossbar by Speiss and Mooney followed up to nod home.
Just three minutes later the advantage doubled thanks to Baudry, who knocked home from close range to meet a Cook corner.
Referee Lee Collins then had to go off injured, with his linesman replacing him in the middle and fourth official Grant Taylor ran the line.
Orient's position of comfort wasn't to last long though as County won themselves a lifeline with 12 minutes left, Hughes steaming in to fire home from 15 yards after Orient couldn't get a ball clear in their box.
Rowlands almost restored the two-goal lead in the final minute when Orient broke following a County corner, weaving through the defence before drawing another save from Speiss,but Orient had already done enough.
Leyton Orient: Jones; Cuthbert, Baudry, Chorley, Sawyer; Odubajo, Rowlands (Smith 90), James, Cook (Cox 85); Mooney, MacDonald
Subs: Griffith, Symes, Grainger (GK), Obafemi, Omozusi
Goals: Mooney 65, Baudry 68
Subs: Kelly, Smith, Mahon, Labadie
Referee: Lee Collins
Attendance: 3,578 (446 away)