Just when it looked like a replay would be needed, the winger popped up at the back post to send Gareth Ainsworth's side through to Monday's third round draw.
It was no more than the Chairboys deserved after a confident performance against opponents nowhere near the top of their game.
Paul Hayes put the away side ahead in the 50th minute when he was given way too much time in the box to finish.
Midfielder Ben Thompson equalised for Millwall seven minutes later when his shot from outside the area flew into Matt Ingram's bottom corner.
Wycombe thought they had gone ahead when Harriman finished at the back post before the strike was ruled out for offside.
But he had the final say when he scored in the fourth minute of added time to send the away hordes into ecstasy.
Byron Webster returned from suspension to partner Sid Nelson in the centre of defence, and there was a real nervousness there during a first half when Wycombe should have gone ahead.
Neil Harris has had to re-jig his defence a number of times this season with injuries and suspensions. Webster started on the left side of the centre-back partnership and didn't look entirely comfortable there.
Mark Beevers has been a constant for Millwall since he switched to centre-back from left-back earlier in the season and his calm assurance was missed. Aaron Amadi-Holloway blew a glorious chance to put Wycombe ahead when he was played in by Harriman but dragged his shot wide with just Jordan Archer to beat.
Archer also had to get down quickly to keep out Luke O'Nien's half-volley as Wycombe dominated the opening period.
You could see Ainsworth's side growing in confidence as the half went on and they often poured into Millwall territory in three-on-three or four-on-four situations, with Matt Bloomfield and Sam Wood getting forward to join the front pair.
At the other end there was space behind Wycombe's back four waiting to be exploited but Millwall were never able to get possession in good enough areas to do it.
It's not a surprise that some tiredness might be creeping in with the current run of fixtures, but it wouldn't have been a surprise either if Harris let them know the display didn't match recent standards at The Den. He certainly wasn't happy in his post-match interview, saying Thompson's goal was the only positive for his side.
Thompson nets his first senior goal
Given that unsteadiness in defence the nature of the opening goal was no surprise. Hayes seemed to have an age to wait for the ball to drop for him before he beat Archer with a low strike.
But Millwall levelled through an unlikely source, Thompson firing in from 25 yards for his first senior goal for the Lions.
He has that ability and had threatened to do something similar a number of times this season.
If the home fans thought that would be the spark, though, they were disappointed. Wycombe were always a danger on the break and their fans were certain they'd retaken the lead when Amadi-Holloway crossed for Harriman only for the linesman's offside flag to halt the celebrations.
The Millwall back four would have been pleased to see Amadi-Holloway go off when he did; he had been a menacing runner all afternoon.
But that respite didn't mean anything when Harriman became the Wycombe hero.
There is little rest for the squad between now and Tuesday night's trip to Southend. And now they'll have to rid themselves of this disappointment as quickly as possible.
In fairness, Harris wasn't using tiredness as an excuse afterwards.
It was a first defeat at home since September 26 when Southend won 2-0 at The Den – and now they face the same side as they attempt to reach the southern section final of the Johnstone's Paint Trophy.
Millwall have travelled to a number of these mid-week games the day before to give themselves every chance of being fresh, but at least this is a short journey.
Southend and Millwall have identical records in terms of points and goal difference in League One, and the Shrimpers stole that win in south London in the second month of the season with their only two shots on target.
Phil Brown's side will also be that bit more rested than their rivals, having had today off after they lost in the first round of the FA Cup to Scunthorpe. They are also on a five-game unbeaten run.
It might work out in the long term this season having one less competition to worry about with a small squad, but Millwall's players won't be thinking like that for the rest of this weekend.