The midfielder scored the only goal of the match on the 29th minute when his slide tackle on the edge of the penalty area ricocheted beyond Morecambe goalkeeper Barry Roche.
The O’s had chances to double their advantage after the break but Payne’s goal was to prove enough as they held on for the slender victory at the Globe Arena.
On the back of Orient’s midweek draw at Luton Town, O’s Head Coach Ian Hendon named the same starting XI as Jay Simpson and Ollie Palmer started up front with John Marquis operating in a deeper role behind.
There was one change on the substitutes bench however as Freddy Moncur replaced midfielder Dean Cox.
It was the first-ever meeting between the O’s and Morecambe, but in truth the opening stages were far from memorable and it was not until the 19th minute that the visitors had their first effort on goal when Ollie Palmer had a header deflected behind for a corner.
Ahead of the clash Morecambe boasted the title as League Two’s top scorers and immediately after Palmer’s chance the Shrimps nearly took the lead when Jamie Devitt got on the end of Paul Mullin’s cross but could only send a header wide of the far post.
As both sides continued to try and grab a foothold on the tie an opening goal did not look to be forthcoming until the 29th minute when Jack Payne benefitted from a slice of luck to register his first Orient goal.
Having seen an attempted pass towards John Marquis intercepted, the Peterborough loanee threw himself towards the loose ball on the edge of the area and was celebrating seconds later as his block flew beyond Barry Roche in the Morecambe goal.
The O’s opener was definitely fortuitous and with seven minutes of the half remaining Bradley Pritchard was nearly the next beneficiary when his cross from the right clipped the top of the crossbar before bouncing behind.
That was to be the final chance of the half however as Payne’s goal proved to be the difference going into the break, but following the restart Paul Mullin squandered a chance equalise inside the opening seconds when he sliced an effort wide from inside the area.
Despite the early warning the O’s responded well and top scorer Jay Simpson had two chances in quick succession as he first poked the ball wide from Palmer’s knockdown before turning well on the edge of the area and drilling a shot wide inches wide of the far post.
With an hour played Devitt then dragged a shot wide from 20-yards and moments later the O’s reverted to a flat 4-4-2 as Lloyd James replaced Marquis.
As the second half wore on the Orient defence continuously frustrated the hosts, repelling anything thrown towards them and on the 83rd minute Alex Cisak was called into action when he tipped substitute Lee Molyneux’s shot round the post.
With time running out the hosts threw everyone forward in search of an equaliser but as the match entered stoppage time Cisak produced a match-winning save to touch Tom Barkhuizen’s shot round the post as the O’s held on for the victory.
The victory keeps Orient 6th in League Two and they now turn their attention to next Saturday when they host Accrington Stanley.
MORECAMBE: Roche, Beeley (C), Edwards, Parrish, McGowan, Kenyon (Kelleher 81), Goodall (Wildig 59), Barkhuizen, Devitt, Ellison, Mullin (Molyneux 68)
SUBS: Thompson, Bondswell, Bailey
ORIENT: Cisak, Clohessy, Baudry (C), Essam, Chicksen, Payne, Pritchard, Moore, Marquis (James 63), Simpson (Turgott 87), Palmer
SUBS: Grainger, Dunne, Shaw, Moncur, Kashket
GOALS: Payne (29)
BOOKINGS: Marquis (24), Chicksen (88)
REFEREE: David Webb
ATTENDANCE: 2,105 (398 Orient fans)