Leading 3-1, just as they were at during Saturday's 3-3 draw at Rochdale, the Sulphurites' fragile back-line was breached three times in the space of 24 minutes by their promotion-chasing hosts, condemning them to a painful defeat.
The visiting team's despair was plain for all to see when Jack Sparkes picked out the top corner of Mark Oxley's net to make it 4-3 with just 10 seconds of five additional minutes remaining.
That moment will however have been just as galling for the hardy bunch of Town supporters who made the 600-mile round trip down to Devon on a Tuesday evening - and those watching on at home.
And Harrogate skipper Josh Falkingham was quick to acknowledge the club's fans when asked about how he and his team-mates were feeling shortly after the full-time whistle.
"We are absolutely gutted and I'm gutted for the fans who travelled down as well," the 31-year-old midfielder told the Harrogate Advertiser.
"I think they deserve a mention. It's a tough one to take, to come all this way on a Tuesday night and they [Exeter] score with the last kick of the game, meaning we end up on the wrong end of a 4-3
"This is a difficult place to come, they are a side who are flying, playing with confidence but the way we started the game, we controlled it. We were 2-0 up and could have had more before the referee gave them a really soft penalty, which he's owned up to as a mistake.
"That's a big moment because he's given them a goal, but we've scored three and could have scored more to really kill the game, however we are finding ourselves retreating, thinking 'let's hold on to what we've got' and maybe that attitude has to be changed.
"When you're in moments in games like that and their crowd are getting behind them, it is difficult, but as players we have got to take responsibility and own up to it because unfortunately we haven't ended up with the result we all wanted."
Goals from Luke Armstrong and Jack Muldoon had Town 2-0 up early on before Jevani Brown converted a penalty which never should have been awarded by bungling referee Brett Huxtable.
George Thomson headed home Luke Page's corner to make it 3-1 shortly after the hour-mark, before Jonathan Grounds pounced on Will Smith's poor touch to reduce the arrears.
Jack Diamond then went clean through on goal and had the chance to end the game as a contest, however, just like Muldoon and Page in the first half, he failed to find the back of the net with just Cameron Dawson to beat.
And those misses were to prove costly as Timothy Dieng levelled matters before Sparkes conjured up that last-gasp winner.
"We could and should have scored more," Falkingham added
"Attacking-wise, when we do get hold of the football, when we manage to make three, four, five passes, we are not just keeping possession, we are actually hurting teams.
"We've come to Exeter and scored three goals, but we've had three one-on-one opportunities as well. We're not talking little half-chances where one has flashed just the wrong side of the goal.
"These are three massive goal-scoring opportunities that we have to be taking."