Pompey were unable to halt Exeter’s resurgence as they fell to defeat against their in-form visitors.
The goal that proved the difference between the sides from David Wheeler owed a lot of good fortune, with a ricochet aiding the Devon outfit.
But the Blues struggled to create many chances of note in their ultimately futile search for a leveller.
Paul Cook unsurprisingly stuck with the same side that beat Leyton Orient on the south coast a fortnight earlier.
That meant Conor Chaplin continued to lead the line alongside Michael Smith in a 4-4-2 formation.
Before kick-off there was a minute’s applause in memory of title-winning forward Lindy Delapenha, who sadly passed away earlier in the week.
There was little to excite another large Fratton crowd once the action got underway, with clear-cut chances at a premium throughout the first half.
The hosts dominated possession, although a well-marshalled defence meant they were not able to test Christy Pym in the Grecians goal.
Chaplin showed some neat invention to try to convert Carl Baker’s cross with a back-flick, but the ball flew wide.
David Forde flung himself to the left to deny Reuben Reid at the other end, then grabbed the loose ball at the second attempt.
Ollie Watkins was looking the most threatening player for the visitors and the sought-after striker drilled a low effort narrowly past the post on 16 minutes.
And Christian Burgess was enjoying a personal tussle with Reid, with the defender making a couple of key challenges inside the box to frustrate his opponent.
There was one more opportunity for Baker to break the deadlock before the break, but his effort was fumbled behind by Pym as a drab opening 45 minutes came to a close.
Exeter City 0
Pompey were first to threaten at the start of the second half, but a poor attempt from Kal Naismith flew over the bar.
The visitors went closer moments later and Enda Stevens had to turn Ryan Harley’s cross behind before Watkins could pounce.
And the Grecians did forge ahead on 57 minutes – although they were aided by a huge slice of fortune.
Reid burst down the centre and when he was dispossessed, the ball ricocheted off Danny Rose and straight into the path of Wheeler, who lashed it into the net.
Cook immediately responded with a double substitution, bringing on Jamal Lowe and Gary Roberts in place of Smith and Baker.
And Lowe tried to add a spark to the hosts’ performance with some tricky footwork, while his cross was headed wide by Matt Clarke.
It was Gareth Evans who forced Pym into action on 72 minutes, however, with a fierce left-footed effort that the keeper did well to smother.
But Exeter then came close to doubling their advantage when Troy Brown met a corner and glanced a header inches wide.
Pompey pushed forward in search of an equaliser and some fans thought a penalty had been awarded when Stevens went down under Jack Stacey’s challenge, although referee Dean Whitestone was instead pointing for a goal-kick.
There were also a host of late corners, which saw Forde come up to provide a different threat, but despite five minutes of added time and the Grecians starting to sit back, the hosts were unable to provide some late drama.
Pompey (4-4-2): Forde; Evans, Burgess, Clarke, Stevens; Baker (Roberts 59), Rose, Doyle (c), Naismith; Chaplin, Smith (Lowe 59)
Booked: Clarke, Forde
Subs not used: O’Brien, T.Davies, Linganzi, Bennett, Hunt
Exeter (4-4-2): Pym; Stacey, Brown, Moore-Taylor (c), Woodman; Wheeler, Taylor, James, Harley; Reid (McAlinden 81), Watkins
Goals: Wheeler 57
Subs not used: Olejnik, Sweeney, Tillson, Croll, Oakley, Simpson
Referee: Dean Whitestone
Attendance: 17,195 (1,010 away fans)