Alex Cisak saved a Chaplin penalty in the opening peruod, but the diminutive striker put the hosts ahead, only for Gavin Massey to net a stunning equaliser for the O's.
However, two minutes into the second period Chaplin scored a decisive header to secure all three points for Paul Cook's side.
The O’s made three changes to the side with Sammy Moore starting following his return from a loan spell with Dover Athletic, while Myles Judd and Sandro Semedo also returned to the starting line-up in place of Yvan Erichot, Callum Kennedy and Josh Koroma respectively.
Orient operated a 3-5-2 formation with Judd and Semedo as wing backs, while Gavin Massey was just behind former Pompey loanee Paul McCallum up front.
Chances were few and far between in the opening stages of the encounter, though the hosts dominated in terms of possession in the final third, without causing the O’s too much trouble.
Alex Cisak’s first action in the game came with 12 minutes on the clock when he held Kal Naismith’s free-kick with Conor Chaplin just failing to get a touch on the effort before the Aussie shot-stopper.
Carl Baker then had space down the right but he fizzed his effort deep into the stand holding the O’s fans as a chance went begging for Paul Cook’s side.
Cisak was again in action as he was forced to tip over a miscued Parkes clearance after Baker had tried to play a throughball for Michael Smith.
It was Pompey creating all the chances and Naismith spurned another opportunity as he skied Smith’s pull back with the goal beckoning.
Cook’s side had a perfect chance to break the deadlock when referee Brett Huxtable pointed to the penalty spot as Moore was adjudged to have brought down Enda Stevens in the box.
Chaplin stepped up to take the spot kick but Cisak pulled off an outstanding save to keep the hosts at bay.
However, there was little Cisak could do two minutes later though when Chaplin made amends and tapped in from close range after Baker’s ball in as the O’s appeals for offside were waved away.
Baker then saw an effort deflected over the bar as Pompey looked to add a quickfire second and the O’s had Tom Parkes to thank as he cleared Smith’s effort off the line.
Chances soon evaporated though, until the O’s found an equaliser with their first shot of the game on 37 minutes, and what a shot it was.
Paul McCallum laid it into the path of his fellow front man Massey who took it first time and curled it straight into the top corner and that is how it remained at the break.
Jamal Lowe came on for his Pompey debut at the break, replacing Gareth Evans and with little over a minute gone in the second half the hosts went in front once more.
Lowe played it back to Baker and his ball in was directed past Cisak by Chaplin to double his and Pompey’s tally.
Two could have become three five minutes into the half when Stevens worked his way into the area and his shot from an acute angle was held at the second attempt by Cisak with Smith ready to pounce for the hosts.
Orient looked to bounce back from the early goal and a lovely ball in from Atangana found the back-post run of Massey who headed back across goal, but David Forde in the Pompey goal was able to beat McCallum to the ball and mop up the danger.
The O’s were almost handed a second equaliser on a plate when a long ball over the top saw Christian Burgess head past Forde who had rushed out of his goal but the effort crept wide of the post with Collins trying in vain to get the slightest of touches to divert the ball into the net.
Orient pushed for the equaliser and brought on striker Jordan Bowery for the industrious Moore who had played well on his return as Orient returned to a more familiar 4-4-2 formation.
Cisak did well for the O’s as Pompey pushed for a third as he got enough on the ball to divert Naismith’s ball in behind for a corner.
Orient remained defiant though and with the scoreline at 2-1 there was always a chance of a way back into the contest.
A throw-in from McCallum found its way to Semedo who played in Massey, who in turn fed Parkes and his deflected ball in was fumbled by Forde, only for the keeper to gather at the second attempt, and up the other end Stevens fizzed an effort wide.
With a minute left in normal time the O’s chucked on Ollie Palmer for Semedo in a last-ditch attempt to force an equaliser, but three minutes of stoppage time came and went as Andy Edwards' side lost out at Fratton Park.
PORTSMOUTH: Forde, Stevens, Clarke, Burgess, Evans (Lowe HT), Baker, Doyle (c), Rose, Naismith (Linganzi 76), Smith, Chaplin (Bennett 87).
SUBS: O’Brien, Davies, Roberts, Hunt.
BOOKED: Doyle (72)
GOALS: Chaplin (23, 47)
ORIENT: Cisak, Parkes Mezague, Hunt, Semedo (Palmer 89), Moore (Bowery 69), Atangana, Collins, Judd, Massey, McCallum.
SUBS: Sargeant, Kennedy, Nnomo, Pollock, Koroma.
BOOKED: Atangana (26)
GOALS: Massey (38)
ATTENDANCE: 16,564 (607 Orient fans)
REFEREE: Brett Huxtable.