Bonne slotted home from the spot in the 42nd minute to notch his 16th league goal of the season to see the O’s back to E10 with the victory.
Head Coach Justin Edinburgh named an unchanged from the side who secured a point last weekend at home against Tranmere Rovers.
The reverse fixture in September 2017 ended 1-2 to AFC Fylde with Danny Rowe notching both goals for the visitors and Jobi McAnuff getting the consolation late in the second half.
AFC Fylde got the game underway in sunny, but very chilly conditions and Fylde front man Danny Rowe fired wide of the target from range after two minutes to register the first attempt on goal of the game.
Fylde continued to enjoy the ball in the early stages of the game with O’s ‘keeper Dean Brill having to be alert to punch clear a Lewis Montrose cross that looked dangerous.
Dan Holman’s first time switch to James Brophy saw the winger cross towards the head of Macauley Bonne but Fylde managed to clear it to the edge of the box where Craig Clay waited and volleyed an effort towards goal only to be blocked by the body of Jordan Tunniclifffe.
In the Orient box, Josh Coulson was present to divert the ball away from danger when Rowe collected the ball on the right and drilled a low cross towards the centre of the box.
As the half hour mark approached the O’s began to control the game, skipper George Elokobi forced a corner from the hosts after Josh Koroma’s deep free-kick caused the Fylde defence problems in the area.
Koroma was involved again minutes later, when Henry Jones received a booking for pulling the winger back as he broke clear down the right wing and had the better of the Fylde man.
Orient certainly looked the better side at this stage and looked the most likely to score when Holman tried his luck from range, but saw the ball drop the wrong side of the crossbar before Brill was quickest to react to Jones’ dangerous free-kick and gather the danger.
Bonne, Brophy and Koroma countered the Fylde back line and the latter opted to go for goal himself and forced a good save from Lynch.
With less than five minutes until the break Dan Holman was brought down inside the box under the challenge of Grand before Orient front man Bonne stepped up to smash passed Lynch to register his 16th league goal this season.
Orient got the second-half underway but it was the hosts who started the on the front-foot, Francis-Angol struck at Brill before the O’s ‘keeper got up well to punch clear a cross that was heading towards an unmarked Grand.
Five minutes after the restart Rowe struck a powerful free-kick wide of the far post from range, as the hosts looked to find a leveller.
AFC Fylde with the upper hand saw Bonne alert on defensive duties to clear the ball off the line when Grand appeared in the box unmarked and headed towards goal.
Grand was involved for the hosts yet again, when the defender swept away the danger after Brophy crossed for the lurking Holman at the back post.
On the hour mark, Koroma embarked on a pitch long run and fired low towards the target but Lynch was there to save with his feet before Holman headed in to the hands of the ‘keeper from Adams’ cross.
Brophy twisted his way in to the box and fired a deflected shot towards goal, the ball just missed the boot of Bonne who waited at the back post for what looked like a sure goal.
Orient’s lead should have been doubled when Brophy again worked his way to the by-line and pulled the ball back for Holman in the centre of the box, but the striker couldn’t connect with the ball cleanly enough to divert the ball towards goal.
Less than ten minutes remained when Clay created himself some space and found Bonne in the box with a beautiful cross but the header flew just wide of the target, as the visitors saw another chance go begging.
Brave defending from Elokobi and Coulson kept the hosts at bay in the dying moments of the game as Fylde saw shots from close range blocked by the bodies of the Orient back two which meant the O’s hung on for the three points.
AFC FYLDE: Lynch, Francis-Angol,Tunnicliffe, Grand (Blinkhorn 76), Burke, Bond (Hardy 65), Finley (C), Montrose, Muldoon (Smith 65), Rowe, Jones
SUBS: Taylor, Chettle
BOOKED: Jones (30)
ORIENT: Brill, Caprice, Elokobi, Coulson, Widdowson, Koroma (Lawless 86), Clay, Adams, Brophy, Bonne, Holman (Harrold 90+3)
SUBS: Grainger, Happe, Reynolds.
BOOKED: Widdowson (44), Caprice (88)
GOALS: Bonne (42)
REFEREE: Karl Evans
ATTENDANCE: 2,206 (326)