Full-time from The Den
Justin Skinner's young charges gave their all against their Premier League opponents, who had the game's outstanding player in Callum Roberts.
The young Lions went desperately close to breaking the deadlock in the opening 70 seconds when skipper Chris Parr's powerful header from a corner was cleared off the line.
Newcastle responded, and quickly got into their stride with the dangerous Roberts drilling wide from 16 yards after good work by team-mate Sean Longstaff.
It was Roberts who earned Newcastle the first of their two penalties in the game, when he was fouled by Lions keeper Harry Girling after breaking into the danger zone. Girling was shown a yellow card for the foul and Roberts made no mistake from the resulting penalty kick, firing the visitors ahead with 18 minutes on the clock.
Keeper Girling came to the rescue just five minutes later, making a great save with his feet to deny Daniel Barlaser at his near post.
But the visitors didn't have to wait much longer for their second goal of the game, with Longstaff producing a cool, clipped finish that gave Girling no chance after the home defence were caught napping.
A strong run into the box by Eberechi Eze on 38 minutes was halted by Newcastle keeper Paul Woolston, who was quick to collect the ball at the striker's feet.
Keeper Woolston was called into action just 60 seconds later as The Lions pushed for a goal, quickly sprinting off his mark to collect the ball under pressure from John-Prince Rylah after he looked to get on the end of Kyron Farrell's forward pass.
Eze produced some super skill to create an opening two minutes before the break, but saw his 16-yard effort flash inches wide of the target before setting up Kris Twardek in a near-identical position, who went even closer with his shot.
Newcastle striker Roberts smacked the woodwork early in the second-half following a quick Newcastle counter-attack, and was then denied his second - and United's third - of the game with a ferocious drive that Girling pushed away at full stretch.
However, the visitors did not have to wait much longer for their third goal of the game when Dexter Peter was very harshly adjudged to have handled when the ball appeared to be driven straight at him from close range. Referee Whittaker pointed to the spot for the second time, and Ben Drennan stepped up to smash home the spot-kick to give the visitors a three-goal cushion.
Back came the young Lions though, and an appreciative home crowd of over 500 played their part in trying to cajole and encourage the youngsters as they kept plugging away to try and find a way back.
Jamie Philpot, Millwall's Man of the Match, grabbed the goal that his excellent performance deserved and when a Newcastle player handled in the penalty area, the young striker made no mistake with a crisp finish from the penalty spot.
Philpot went desperately close to adding a second in the 90th-minute with a neat piece of control and shot that took a deflection for a corner as The Lions pushed forward trying to claw back the two-goal deficit.
Sadly time, and luck, was not on their side and the final whistle blew bringing an end to Millwall's hopes of progressing through to the Fourth Round despite their gallant effort.
Newcastle United: Woolston, Williams (Cobain, 66mins), Gibson, Drennan, Newberry, Cameron, Barlaser, Ward, Roberts, Longstaff, Heaney. Subs not used: Pearson, Laidler, Holmes, Charman, Hunter, Pollock.
Ref: J Whittaker
Don't forget to vote for Jamie Philpot and JP Rylah in the LFE November Goal of the Month competition here