Following a tight first half, Mooney opened the scoring with a brilliant header on the hour before the points were sealed in the first minute of stoppage time as substitute Boco stroked home his first for the Club.
Steve Davis named an unchanged side from Tuesday nights impressive victory over Solihull Moors, a performance he would have wanted to mirror prior to kick-off.
The O’s started the game brightly and enjoyed large spells of possession but the only clear cut chance came when the ball fell to Macauley Bonne inside the box, who couldn’t connect with Joe Widdowson’s cross enough to direct it towards goal.
20 minutes in and Maidstone had their first chance, when a ball over the top split the Orient defence and Joe Pigott was clean through on goal before the on-rushing Charlie Grainger closed down the shot and Tom Wraight placed the rebound in to the stands.
At the half hour mark, Orient had the greater of possession out of the two sides, but both were being restricted to long range efforts as the defences stood strong.
Minutes before half-time, Orient managed to create a chance as a result of all the pressure. Mooney’s flick off found Jobi McAnuff who forced his way in to the area and fired a low shot into the hands of Lee Worgan in the visiting goal.
After the break, Orient picked up where they left off. Jake Caprice crossed the ball towards Bonne who flicked it up for Mooney but the strikers attempted overhead kick was blocked by Maidstone defender Josh Hare.
Orient were pressing for an opener as Bonne showed great pace to leave his defenders before entering the box but the striker dragged his shot just wide of the goal.
A rare Maidstone chance came when the ball was headed over Grainger’s goal by Wraight at the far post.
A goal was looming at Brisbane Road and Orient finally got the opener when James Dayton’s early cross found the head of Mooney who found the back of the net with a superbly placed effort.
Orient continued to push for a second as Dayton’s deep free-kick was headed behind for a corner before Bonne fired over the second ball from the penalty spot.
Another attack down the right, this time Caprice’s low driven cross is met by Bonne who’s touch rolled just wide of the post.
Two changes for Orient were made in the 79th minute, introducing Josh Koroma and Craig Clay for Mooney and McAnuff. Winger Koroma made an instant impact shaking off two defenders before his effort curled just wide of the post.
As the match entered the closing stages Maidstone continued to push for an equaliser,and thought they had equalised a minute before the end when Delano Sam-Yorke smashed home from close range after Pigott had been brilliantly denied by Grainger.
Despite reeling away in celebration, the Maidstone forward was left with his head in his hands when he saw the flag had been raised for offside.
Having survived the late scare, Orient then sealed the victory in the first minute of stoppage time when substitute Romuald Boco was on hand to put the game beyond doubt with a composed finish from inside the area following great work from Lee.
Orient are next in action away to Bromley on Tuesday night where we will be looking to build on the back-to-back victories.
ORIENT: Grainger, Caprice, Coulson, Elokobi, Widdowson, Lawless, Lee (C), Dayton (Boco 86), McAnuff (Koroma 79), Mooney (Clay 79), Bonne
SUBS: Sargeant, Clark
GOALS: Mooney (60), Boco (90+1)
Booked: Widdowson (24)
MAIDSTONE: Worgan (C), Hare, Prestedge (Willard 74), Wynter, Sam-Yorke, Paxman, Wraight (Richards 80), Anderson, Reason, Nana Twumasi, Pigott
SUBS: Taylor, Okuonghae, Phipps
BOOKED: Prestedge (40), Paxman (57)
Referee: Adam Bromley
Attendance 5,085 (595)