Full-time score from The DenTwo goals from Chesterfield's Jay O'Shea condemned Millwall to a fourth successive home defeat of the season and continued a miserable run that has seen The Lions win just three times on home soil since October 2014.
Whilst O'Shea's 17th-minute opener was a goal good enough to grace any stage, a wonderful first-time volley, his second in the dying seconds of the game took a huge deflection on its way past the wrong-footed Jordan Archer.
Millwall started with five academy graduates in the team, but showing just one change from the last starting XI with Jack Powell replacing Shaun Williams in midfield for his first League start of the season.
However the nervy Lions were taken to task by their opponents who bossed proceedings for much of the opening half, and were equal to everything a much improved Millwall threw at them in the second.
There was less than two minutes on the clock when Powell worked space on the left flank and sent over an inviting cross, but there were no Lions players on hand to attack the ball.
That pretty much proved to be the sum total of Millwall's attacking threat in a poor opening half an hour in which the visitors dominated matters, frustrating both the home team and fans with the amount of possession they had.
It took a couple of excellent early defensive blocks from Sid Nelson to clear the lines as Chesterfield continually stretched the Millwall defence. Jordan Archer came to the rescue with a smart save after five minutes, holding Ian Evatt's powerful header from Gboly Ariyibi's cross as Dean Saunders' team looked for a way through.
But there was little the Lions keeper could do to prevent Chesterfield taking the lead following a spell of pressure in the 17th-minute. A routine cross was headed clear by Nelson but the ball fell invitingly for O'Shea, who hit a cracking first-time volley that flew into the back of the net from 18-yards via the foot of the post.
It could have been even worse for The Lions seven minutes before the break of an instantly forgettable opening half. A slip by Ben Thompson enabled Dan Gardner to win possession and slide a neat ball through to Sam Morsy, who was one-on-one with Archer. The Millwall keeper did superbly to spread his body and divert Morsy's goalbound effort away for a corner.
Manager Harris wasted little time making changes in a bid to liven up the team, introducing Aiden O'Brien for Lee Gregory and the Academy graduate certainly made an impact and was involved in the best of Millwall's attacking moves.
Twice Fred Onyedinma was narrowly caught offside from probing through balls On 59 minutes Onyedinma touched the ball into Jimmy Abdou's path, and his cross was headed clear off the line.
Despite enjoying more possession, it was Chesterfield who nearly carved out a second goal in the 67th-minute on the counter. Sylvan Ebanks-Blake played in O'Shea but the midfielder's tame shot was held by Archer.
Millwall kept plugging away trying to find a way through and it looked as if The Lions' persistence was going to pay off with 16 minutes remaining.
The ball was floated into the penalty area and Abdou reacted quickest at the far post, only for keeper Tommy Lee to brilliantly paw his shot away with a reaction save.
Harris introduced Paris Cowan-Hall a couple of minutes later and the home fans were off their feet when the sub was sent sprawling after spinning clear of his marker in the 82nd-minute. To the fury of the Millwall camp referee Darren Deadman controversially waved play.
On came John Marquis with the third and final roll of the dice and the presence of another frontman ruffled Chesterfield feathers as The Lions kept pushing in search of that elusive equaliser.
It so nearly arrived in the final minute of normal time when O'Brien's exquisite flick picked out Onyedinma in front of goal, but in a move that summed up Millwall's afternoon, the ball spun off the teenager's shins and was collected by keeper Lee.
Chesterfield were a whisker away from doubling their tally with a 93rd-minute angled shot from Armand Gnanduillet that flashed a foot wide.
However Saunders' men grabbed a second goal with virtually the last kick of the game; Dieseruvwe broke, squared to O'Shea whose shot took a deflection before agonisingly bobbling over the line.
Millwall: Archer, Cummings (Marquis, 86mins), Craig, Beevers, Nelson, Powell (Cowan-Hall, 76mins), Thompson, Abdou, Morison, Gregory (O'Brien, 46mins), Onyedinma, Subs not used: Forde, Williams, Upson, Webster.
Chesterfield: Lee, Jones, Hird, Morsy, Evatt, Gardner (Raglan, 87mins), Martinez, Ebanks-Blake (Gnanduillet, 72mins), O'Shea, O'Neil, Ariyibi (Dieseruvwe, 72mins). Subs not used: Cairns, Humphreys, Raglan, Harrison, Banks.
Ref: D Deadman
Att: 8,374 (away 508)