Full-time from The Den
Paul Hayes had fired Gareth Ainsworth's side into a 50th-minute lead, but that advantage lasted just eight minutes with Ben Thompson firing home his first goal for The Lions to level matters up.
However with Neil Harris' side temporarily down to 10 men as Alfie Pavey waited to come on as a sub for the injured Fred Onyedinma, Harriman took full advantage and drilled home the winner with seconds remaining to spark wild celebrations in the visiting camp.
Then, three minutes before half time, Harriman's ball in from the right found the unmarked Amadi-Holloway, but he poked his effort wide of the far post with the goal gaping.
After a goalless first half, and probably a word or two from manager Harris at the break, The Lions certainly livened up after the break and in the first three minutes created more opportunities on goal than the whole of the previous 45 minutes.
A neat one-two between Upson and Williams ended with the latter's shot stinging the palms of keeper Ingram, whilst O'Brien lashed the ball over from a central position as Millwall pressed for the opener.
But the wind was knocked out of their sails on 50 minutes when, following a quick counter-attack, Hayes was on hand to steer the ball home from close range giving Archer no chance.
That joy was short-lived, however, and eight minutes later Thompson celebrated his first senior goal for his boyhood club latching onto a half-clearance from Wycombe and thumping a half-volley into the bottom left corner.
That should have given Millwall the impetus to go on and win this tie, but Harris' charges just couldn't get into their attacking rhythm and Wycombe resolutely stuck to their job, frustrating the home side and giving them little time to settle on the ball.
Harriman gave an early warning of his intent, sweeping home in the 61st-minute following another incisive break from the visitors, but on this occasion the linesman's flag came to the rescue and his effort was ruled out for offside.
Thompson was close to grabbing his second after 67 minutes with a well-worked corner move after being picked out by Shaun Williams, but he hesitated slightly before taking aim and drove narrowly wide from 16 yards.
The Lions brought on Fred Onyedinma and the youngster was a whisker away from connecting with a super through ball from Gregory, but the ball was swept behind for a corner.
Onyedinma's presence certainly looked to unsettle the Wycombe defence, although unfortunately his contribution came to an abrupt halt when he sustained a back injury following an off-the-ball incident that left the youngster in need of treatment.
Although he continued to play on, Onyedinma was forced off in the 94th minute and it was during this period with The Lions down to 10 men and trying to get sub Pavey on the pitch, that Wycombe struck a last-gasp winner.
Edwards challenged for the ball on the edge of the penalty area, went down injured and as play continued, the ball broke on the left. Sam Wood and Aaron Pierre combined to set up Harriman, and the QPR loanee made no mistake from close range to shatter Millwall's FA Cup dreams and secure their place in the Third Round draw.
Bookings: L.Martin (88mins), Thompson (90+2mins)
Scorer: Thompson (58mins)
Bookings: Pierre (51mins), Hayes, (65mins), Stewart (72mins), O'Nien (86mins)
Scorers: Hayes (50mins), Harrison (90+4mins)