Careless Pompey let more precious points slip from their grasp at the death in another miserable midweek trip.
Paul Cook’s side appeared to be heading for a 1-0 victory when the clock showed 90 minutes, albeit under some intense pressure.
On the night Paul Tisdale was presented with a silver plate to mark 502 matches in charge, the youngest player on the pitch intervened.
Conor Chaplin was a mere nine years and four months in the Blues’ Academy when it all began at Exeter for the long-serving boss.
And on 31 minutes, clever control culminating in a cool finish into the bottom corner of the home net saw the Worthing youngster notch his ninth goal of the season.
Cook had labelled the welcome Saturday victory over Cambridge United as winning ugly.
Last night they looked set to win uglier.
Then Ollie Watkins cut in from the left, brilliantly negotiating a number of challenges before finishing from a tight angle.
A marvellous strike from the youngster and certainly deserved for the Grecians, who were the superior side in the second half as they chased the game.
Once again operating with a 4-4-2, the Blues represented a solid, well-organised unit possessing no frills.
However, it was the Grecians who provided the more enterprising play, retaining possession far better and, during the second half, dictating play.
Aside from two misplaced headers from ex-Pompey striker Jayden Stockley, though, Ryan Fulton was never truly threatened – then Watkins struck.
The keeper afterwards even had to produce a superb late save to deny Alex Nicholls’ free-kick.
And the opposition manager who took over the reins in June 2006 had his late, late point.
There were no changes to the Blues side which defeated Cambridge United 2-1 at the weekend.
With no fresh injury worries and none of the walking wounded ready to return, Cook had the relative luxury of sticking to his winning formula.
The substitutes’ bench was also unaltered, eight-goal Gareth Evans once again on the bench alongside the likes of Matt Clarke and Ben Tollitt.
Once more there was no place for injured quartet Gary Roberts (hamstring), Adam McGurk (back), Michael Smith (calf) and Brian Murphy (calf).
Exeter included former Pompey loanees Stockley and Lee Holmes in their starting line-up.
Stockley departed Fratton Park in January following two goals in 12 games, since netting five times for the Grecians.
Tisdale’s side also included former Southampton skipper Matt Oakley, now aged 38 and last night occupying a midfield position having been pushed up from the centre of defence.
When the match kicked off, Pompey should have taken the lead after only 22 seconds.
Kal Naismith found space down the right and his right-foot delivery picked out Conor Chaplin unmarked at the far post.
The youngster attempted the control the ball on his chest, yet only succeeded in letting it bounce off him giving keeper Bobby Olejnik the opportunity to gather comfortably.
Exeter won the first corner of the game on six minutes when Ben Davies put out a dangerous cross from the right under pressure from David Wheeler at the far post.
The left-wing flag kick was delivered by Holmes, but Wheeler’s subsequent header flew well over the crossbar.
Pompey had their own corner on 12 minutes when Davies’ delivery from the left was met with a back header from Christian Burgess which never threatened the keeper.
There was a bizarre moment on 19 minutes when Kyle Bennett floated a cross in from the left and Holmes volleyed the ball to his own keeper.
Olejnik gathered well, yet his team-mate’s pass was clearly hit considerably stronger than he had anticipated.
On 25 minutes the Blues had their first shot on target following Davies’ corner from the left.
The ball fell for Michael Doyle, whose fierce left-foot half-volley was parried superbly by Olejnik low down and a defender helped complete the clearance.
At the other end, Stockley had a great chance to break the deadlock from Christian Ribeiro’s cross, yet placed his header straight at Ryan Fulton.
Yet on 31 minutes Pompey took the lead, through Chaplin’s ninth goal of the campaign.
While positioned on the edge of the area, the youngster cleverly controlled the ball on his chest and placed it into the bottom of the net.
Moments later, a break from Marc McNulty down the right saw he pull the ball back but Chaplin scuffed his shot when he should have done better.
The Grecians should have been level, however, on 42 minutes with Stockley again proving wasteful.
The impressive Ribeiro gallopped down the right and the on-loan striker from Bournemouth somehow headed past the far post when well-placed.
Then Ollie Watkins cut inside to fire in a right-foot shot beaten out by Fulton as the visitors came under increasing pressure.
After a slow start to the second period, a Grecians corner did spark a scramble in the visiting penalty area, but Fulton soon mopped up by gathered the loose ball.
On 58 minutes, Naismith cut infield and drifted past two players before firing a left-foot shot from distance which was not too far wide of the target.
Then McNulty lofted a ball forwards into the path of Chaplin, prompting Olejnik to come off his line and spark a scramble in which the keeper’s leg deflect a shot just past his own post.
In response, Stockley sent another chance begging when, with back to goal and Webster marking, he did well to spin only to steer a shot wide of the left-hand post.
The hosts made a double substitution on 65 minutes with Joel Grant and David Noble replacing Brown and Stockley.
Naismith won a free-kick off Watkins on the edge of the area on 70 minutes.
But Chaplin’s direct left-foot shot whistled narrowly over the bar.
Then as the game entered 90 minutes, Watkins struck to break Pompey’s hearts.
But it took a magnificent save from Fulton from Alex Nicholls’ free-kick to prevent defeat in four minutes of stoppage time.
And the visitors once again had thrown away more late points.