The goals came at the culmination of a second-half admittedly dominated by the hosts, albeit with Palace unfortunate to see no fewer than four outfield players withdrawn through injury.
Indeed, a more even first-half had seen Palace enjoy the better of the play, Jesse Derry reacting sharply after seven minutes to score his second goal in as many games.
But Chelsea’s late siege – despite the best efforts of Billy Eastwood in the Palace goal, who produced several outstanding saves – was capped by a late McNeilly brace to ultimately snatch the three points deep into stoppage time.
Coming into the game off the back of a 5-0 win over Southampton the previous week, Rob Quinn introduced two new scholars to his starting XI: Kai-Reece Adams-Collman and Zack Henry both enjoyed their first starts at U18s level.
It was the latter who was involved straight away, cutting inside with just four minutes on the clock and firing a fierce rising drive which was beaten away with two hands by Chelsea ‘keeper Luke Campbell.
And Henry was involved seconds later as Palace took an early lead. Hindolo Mustapha nicked the ball on the halfway line and Henry sent captain Zach Marsh sprinting down the right. The forward’s momentum took him away from goal, but his powerful effort was too hot for Campbell to handle, allowing Jesse Derry to steal in and calmly convert.
Initially stunned, Chelsea grew into an absorbing first-half, chances freely flowing at either end of the pitch at Cobham.
Eastwood began what would later become a personal battle with a number of Chelsea attackers with three impressive stops in quick succession, first denying Michael Golding’s fierce strike, then Ato Ampah’s low placed effort, and then Golding again.
The two teams were going at one another hammer and tongs, and a pair of defensive errors led to two more clear chances: another Mustapha interception saw Matteo Dashi’s curling strike denied by Campbell, and then straight up the other end, a Palace slip allowed McNeilly to run clean through – only for his placed shot to clip the outside of the woodwork.
A rapid start was stemmed somewhat by Palace’s first injury of the afternoon, with Henry – impressive in the early stages – withdrawn on 25 minutes after a coming-together with a Chelsea player.
Shortly before half-time, Derry thought he had scored his second, latching onto a long ball into the box after challenging Kaiden Wilson – but he was denied by the referee’s whistle after what appeared to be minimal contact with the defender.
Chelsea pressed for an equaliser before half-time, McNeilly stinging the palms of Eastwood; Jake Grante and Mofe Jemide smothering a shot from Tyrique George; and Golding somehow turning wide from Ampah’s low ball in.
It was a pattern which continued into the second-half, although Palace came close to doubling their advantage when substitute Sebastian Williams’ low clever finish whistled past the post and a goalmouth scramble from a corner saw Chelsea need to clear the ball off the line.
Yet as the second-half wore on, Chelsea’s dominance grew – and further injuries for Palace, to Derry and Cormac Austin, did not help their cause.
The onslaught continued. Seconds after Eastwood denied George’s powerful effort, Palace could only half-clear and, from edge of the area, Russell-Denny side-footed towards the top corner – only for the ball to rattle off the top of the crossbar and over.
Palace’s respite was temporary. Seconds later, a kind break of the ball in midfield allowed Russell-Denny to play in McNeilly, and the Chelsea No. 9 – peeling off his defender – swept a clinical first-time left-footed finish across Eastwood and into the bottom corner.
Despite the Eagles continuing to battle for every ball, Chelsea’s momentum did not stem. George beat Whyte to the byline and clipped a cross towards the penalty spot which – met on the volley by Ampah – was somehow kept out by a simply brilliant flying save by Eastwood.
And after Dashi became the fourth enforced change for Palace, Chelsea’s Travis Akomeah somehow conspired to head the corner over from close range, before Eastwood produced another sharp reflex save from Somtochukwu Boniface’s deflected effort.
Despite further stoppages with injuries, the chances continued in stoppage time, an unmarked Ampah heading wide inside the six-yard box with the goal at his mercy.
It was in the 99th minute that McNeilly completed Chelsea’s late turnaround, stabbing home inside the six-yard box after a speculative ball in had been turned back across the face of goal by Harrison Murray-Campbell.
Rob Quinn's side will hope to recover from a first defeat of the season when they host Reading at the Academy in a week’s time.
Palace: Eastwood (GK), Whyte, Grante, Jemide, Adams-Collman, Austin (King, 82), Dashi (Elliot, 88), Mustapha, Derry (Redhead, 72), Marsh, Henry (Williams, 25)
Subs not used: Hill (GK)
Chelsea: Campbell (GK), Wilson, Akomeah, Boniface, Murray-Campbell, George, McMahon (Runham, 90+7), Golding, Ampah (Mheuka, 90+7), Russell-Denny, McNeilly
Subs not used: Crampton (GK), Olagunju, Chibueze
