Having had to settle for a point on the road at Rochdale on Saturday afternoon despite seeming in control of proceedings, the Sulphurites’ leaky back-line was breached three times in the final 24 minutes of Tuesday's contest, leaving them empty-handed.
And Simon Weaver’s men once again have only themselves to blame, continuing their recent habit of gifting away worryingly soft goals while also passing up a glorious opportunity to put the game to bed while they still held the lead.
Just as was the case at Spotland last time out, Town silenced the home crowd inside five minutes as leading marksman Luke Armstrong picked out the bottom corner to register his first goal in 14 League Two appearances.
Things got even better for the visitors on 18 minutes when Josh Falkingham diverted the ball across the face of goal following a left-wing corner and Jack Muldoon was on hand to turn in from close range.
Having changed formation and begun to ask some questions of the Harrogate defence, the Grecians were then handed a route back into the contest when Devon-based official Brett Huxtable awarded them a questionable penalty, which Jevani Brown dispatched.
Town could have added a third on the stroke of half-time when Jack Diamond broke down the right before squaring a pass to the unmarked Lewis Page, though the former Exeter defender couldn't find a way past Cameron Dawson in the home goal.
They would however restore their two-goal cushion shortly after the hour-mark, George Thomson nodding home Page's inviting corner from the left.
But, within seven minutes, City had pulled one back, Jonathan Grounds pouncing on Will Smith's poor touch inside his own box and firing through a crowd of bodies.
Diamond then went one-on-one with Dawson and looked set to end the game as a contest, but despite having time to pick his spot, he stroked a low effort just the wrong side of the far post.
The on-loan Sunderland winger was guilty of missing a similarly inviting chance at Rochdale, and his profligacy once again proved costly.
Leon Legge switched off to allow Timothy Dieng time and space to head home Jake Caprice's right-wing centre to level matters in the 81st minute as history looked to be repeating itself.
But, on this occasion things were to get even worse for the Sulphurites as Exeter moved the ball from right to left for Jack Sparkes to pick out the top corner with a cultured finish, settling matters with just 10 seconds of five added minutes remaining.
Defeat sees Harrogate drop two places to 15th in the League Two standings.