The prolific Liam Kelly scored his third in as many games to give the O’s the lead at the break, and though Kevin Ellison levelled for the hosts, Bowery’s first goal for the club sealed a welcome three points for Andy Hessenthaler’s side.
Orient made four changes from the side which beat Stevenage 3-1 in midweek with Alex Cisak, Yvan Erichot, Liam Kelly and Gavin Massey all returning to the starting line-up, while new signing Ulrich Nnomo was on the bench having received international clearance.
The work of the O's academy was also evident on the bench with no fewer than five on the bench, including second year scholars Josh Koroma and Myles Judd, while Steven Alzate also travelled to the Globe Arena.
It was a positive start from the visitors, and within the opening few minutes a ball through from Weir almost put Jordan Bowery through on goal, but Shrimps goalkeeper Barry Roche was able to come out and gather.
Despite the strong opening, Morecambe got the first shot away and it was close from Cole Stockton as he flashed the effort across goal and despite Alex Cisak being at full stretch the effort fell wide of the target.
Morecambe worked their way into the game, and goalkeeper Cisak had to be at full stretch to deny Kevin Ellison after 18 minutes from his shot across goal, before birthday boy Nicky Hunt mopped up the rebound.
Orient survived the period of pressure and the O’s closest effort of the half to date as Bowery got a shot away from the edge of the box and a deflection saw it creep just wide of the target.
And it wasn’t long before the visitors took the lead on the 28-minute and you can guess who it came from – striker, sorry midfielder, Liam Kelly.
Twenty-five yards from goal the former Oldham man took one touch before curling an effort into the bottom corner past the outstretched dive of Roche in the Shrimps goal as the 26-year-old scored for the third successive league game.
He wasn’t far away from adding to his tally just four minutes later, but this time the effort was just over the bar.
Chances soon became few and far between and the closest Orient came to doubling their lead was with a quick breakaway from Massey and with very few options he took it on himself and curled an effort wide.
Hunt was then there to block a Jack Dunn strike, before Stockton’s weak effort was comfortably held by Cisak as the game entered the final minute of the first period.
The second half was only two minutes old when Orient almost doubled their lead when a well-worked free-kick saw Robbie Weir force a top save from Roche as he got down low to his right to keep the effort out.
It proved to be a crucial save as the Shrimps went up the other end and only two minutes later levelled proceedings as the ball fell invitingly for Ellison 25 yards from goal and he curled a fine effort past Cisak.
The goal didn’t deter the O’s though as Bowery was presented with a one-on-one opportunity against Roche and the keeper managed to get a touch on it as it struck the side netting and behind for a corner.
Morecambe’s leveller seemed to bring the best out of the O’s and with 54 minutes on the clock they were back in front once again.
The ball fell to Bowery just inside the box and his shot took a wicked deflection on its way into the net.
Two was almost three as Cornick delivered a lovely ball into the box and a sliding McCallum met the delivery only to see it deflected wide of the goal.
A one-goal lead is always precarious and home skipper Michael Rose was just inches away from levelling matters as he fierce effort was just off target, while penalty appeals were waved away up the other end when McCallum went down in the box.
The O’s centre backs were rampaging forward within a matter of minutes as Erichot set up another attack, before minutes later his partner in crime Parkes went forward and saw his header held by Roche.
Orient were knocking on the door for the third as McCallum and Bowery launched another attack with the former playing in the latter who saw his effort saved by the feet of Roche, before a fluffed Massey shot was blocked by the home defence.
Erichot almost opened his goalscoring account when getting on the end of skipper Weir’s corner as the O’s continued to remain on top.
As time ticked away the hosts were pushing for the leveller and the O's had to withstand large chunks of pressure, however they were remaining defiant and despite a minimum of four minutes added on at the end of the game, Orient were able to end the week with a welcome victory.
MORECAMBE: Roche, Wakefield, McGowan, Edwards, Barkhuizen, Ellison, Whitmore, Fleming (Kenyon 64), Dunn (Turner 64), Stockton (Mullin 86), Rose
SUBS: Nizic, Molyneux, Massanka, Jennings
GOALS: Ellison (49)
BOOKED: Rose (66), Ellison (90)
ORIENT: Cisak, Hunt, Parkes, Erichot, Kennedy, Massey, Kelly, Weir, Cornick, McCallum, Bowery
SUBS: Sargeant, Palmer, Nnomo, Semedo, Pollock, Koroma, Judd
GOALS: Kelly (27), Bowery (55)
BOOKED: Bowery (90)
REFEREE: John Brooks
ATTENDANCE: 1,665 (257 Leyton Orient fans)