The Isthmian premier division side, who were beaten by Horsham in the final of this competition last season, came into the match on the back of a 2-0 win against Bognor at the weekend which snapped a sequence of three league losses on the spin.
Chichester, in fine form of late, had lost only once in nine games in all competitions.
The bulk of Margate’s starting XI here featured in that Bognor match, but there were eight changes to the Chi side that lined up in the 1-1 draw with Sittingbourne last time out. Issac Bello and Eric-Georges Dellaud got the nod at right and left back respectively; Joe Moore, whose wonder-goal helped the hosts past Haywards Heath in the previous round, started in centre mid; and regulars Lewis Hyde, Lloyd Rowlatt, Ben Mendoza, Olly Munt and Callum Overton all returned.
After a minute’s silence observed ahead of Remembrance Sunday Kieran Magee was the first keeper called into action as Margate pressed early doors, palming the ball away for a corner.
Dellaud blocked and conceded another one which Magee punched clear for a follow-up cross that was too deep.
Ethan Prichard’s run opened things up as Chi countered and silky skill and a neat back-heel to Mendoza resulted in a delivery which the visitors smuggled away.
Eddie Dsane, who certainly had some wheels, caused Ben Pashley a problem or two with his pace, but the Chi skipper dealt with his first raid five minutes in.
Dsane threatened sixty seconds later as Gate went direct again only for Prichard to challenge Taylor Fisher effectively.
Magee was then out smartly to clear a diag from the right and City won a corner that came to nothing before Moore made an excellent sliding tackle.
Sam Blackman hooked up with James Bessey-Saldanha who fired an effort high and wide.
Next, Dsane received some lengthy physio treatment after a strong challenge and Fisher was well-in on an advanced Prichard.
Both teams cancelled each other out in a 10-minute spell or so played out predominantly in the middle of the park.
Munt picked Dellaud for an attempt that was blocked; Moore was in sharply on Fisher; and Mendoza tried his luck but Daniel Jinadu saved easily enough.
Following Harry Hudson’s air-shot on 34 minutes Jinadu got behind Munt’s effort and then the Chi player won a phantom corner moments later after a swing and a miss.
Jinadu flapped at this somewhat but managed to get a glove of sorts on it for another one on the other side which he claimed comfortably this time.
A lackadaisical pass from Jinadu’s counterpart put Dellaud in trouble and resulted in the first yellow card of the evening and a free-kick for the Gate in a dangerous position.
Bello though headed this away at the back stick for a corner and Ethan Kaiser wasn’t far off with a bullet header at the near post.
Munt and Prichard combined in a slick move in time added on that ended with Prichard cutting back out of reach of teammates.
Deslandes came on for Kaiser at the break and a characteristic Bello charge saw him dance past an opponent or two before finding Mendoza. The Chi midfielder though chose not to shoot first time and lost possession over-playing.
Fisher and Bessey-Saldanha then got in down the left flank and the latter squared the ball to Gate captain Ben Greenhalgh whose effort was diverted for a corner.
Next, Hyde tidied up ahead of Dsane; Overton was guilty of a poor touch to a cross-field pass; and Pashley made a superb intervention to deny Greenhalgh.
Chi had to contend with the Step 3 side’s high-press.
Prichard, who for whatever reason doesn’t seem to get many of these, won a free-kick following Hudson’s crude challenge and then linked up with Mendoza but after jinking this way and that was unable to produce any end product.
Hyde then made an excellent recovery to deny Deslandes and his CB partner Pashley’s towering header cleared a corner.
Overton couldn’t keep a shot down on 64 minutes that fizzed inches over the bar and at the other end Magee missed a cross up against Greenhalgh and Cameron Brodie dragged a shot wide.
First Hyde, then Pashley and finally Rowlatt all headed away as Margate enjoyed their best period so far before Blackman blazed over.
Greenhalgh played a corner short to Bessey-Saldanha and delivered the return pass poorly.
Bello was at it again with a determined run only for Prichard to cut inside and skew one off target.
Bessey-Saldanha and Harrison Hatfull carved Chi up. Did Dellaud catch the Gate No2? Referee Andrew Dunn didn’t think so.
Next, Prichard teed up Overton but the hosts’ striker should have put his foot through it.
Bello dealt with a couple of tricky balls into the box before a slip by Moore, and perhaps some obstruction by the ref, ended with Deslandes stroking the ball past Magee for the only goal of the game.
Both sides rang the changes; Gate sub Troy Howard played a wayward cross; Rowlatt headed clear a corner once again; and Peter Ojemen joined Dellaud in Mr Dunn’s notepad.
Bessey-Saldanha failed to trouble Magee with a tame shot six minutes from the end and then Ethan Robb, who’d replaced Rowlatt was well in to block Deslandes’ effort.
Munt and Joe Clarke, on for Moore, exchanged passes in the three minutes of time added on and fellow sub Rob Hutchings wasn’t far off with the last shot of the game.
So, Chi exit the competition at the same stage as last year where they lost 5-3 to Folkestone Invicta who Margate now face in the next round.
Up next for the Oaklands Park outfit is a league match away at Haywards Heath on Saturday 12th November (Kick Off 3pm).
Chichester – Magee, Bello, Dellaud, Moore, Hyde, Pashley, Rowlatt, Mendoza, Overton, Munt, Prichard (Cody, Clarke, Robb, Hutchings, Clack).