Pompey fell to their second home defeat of the season in a game that highlighted the problems that have blighted them all season.
For all of their dominance in the first half, the players' profligacy up front meant they missed countless chances to wrap the match up by half-time and both of Notts County's goals hammered home just how deficient Paul Cook's defenders can be as a unit.
There were early chances for Pompey to take the lead, none more so than Conor Chaplin's glaring miss from just yards out after Enda Stevens had put the ball on a plate for him.
The 19-year-old then had another great chance after being put through on goal only for his shot to be saved by Adam Collin. He then slipped up before he could reach the loose ball and the danger was gone.
Carl Baker also forced a save from the Notts County keeper and it looked like a goal was coming. And it did, but it was for the visitors as a quick free kick was collected by Adam Campbell and the players seemed to stand still as he curled the ball past a static David Forde.
It was a terrible goal to concede but most fans would have backed Pompey to come back and it took just three minutes to restore parity as Kyle Bennett took advantage of some slack defending and passed the ball to Gary Roberts in the box who squared it for Chaplin who couldn't miss, despite his two failed attempts earlier in the game.
The home side continued to dominate and create chances but the scores were level at the break. A betting man would have lumped on Paul Cook's men coming out in the second half and putting County to the sword.
However, what followed was a turgid display as John Sheridan reorganised his troops and Pompey struggled to break them down.
A bad half turned worse when County took the lead for the second time in the match and once again it was a poor goal to concede as the ball was headed towards goal, Burgess failed to win it and allowed it to run to Jonathan Forte who squared to an unmarked Campbell who slotted past Forde.
The Pompey keeper was booked for protesting that Tom Davies had been fouled in the build-up but it would have been a soft one to give. What wasn't soft was the red card soon after for Aaron Collins who produced a dangerous late lunge on Forde.
Having the man advantage meant that the eleven men of Pompey created the majority of the chances towards the game's end, but they still could have been punished on the break had the Magpies been more clinical.
As it was, Curtis Main wasted a good opportunity to equalise by planting his header straight at Collin and then the Notts keeper produced a great save to deny Baker as he tipped his shot over the bar from close range.
From the corner, Baker fired the ball over the bar and there was one final chance for Roberts but his shot fizzed wide of the post. The final whistle blew and the team were booed off for such a poor second half performance.
The fingers of blame were being pointed at various people as angry Pompey fans left Fratton Park. The manager took most of the stick and some of it was warranted.
Cook's problem is that whilst his plan A works quite well, once the opposition have sussed it out, he doesn't have a plan B. His substitutions also have to be called into question for two reasons.
Firstly, his like-for-like changes didn't change the formation of the team and therefore allowed County to lock the game down until they were reduced to ten men. And secondly, he brought off two of Pompey's best players on the afternoon in Bennett and Chaplin rather than someone like Roberts who was virtually anonymous or even Michael Doyle who has been sluggish in recent games.
That is a worry, as without his protection an already flimsy back four are going to be even more vulnerable. Yesterday's game was the sixth from fourteen league games that Pompey have conceded two or more goals and the last eight games have only yielded a single clean sheet. Amine Linganzi performed well but maybe it's time to give the skipper a break and let the more mobile Danny Rose start the next game?
Burgess and Davies at the heart of Pompey's defence still lack organisation and there will be question marks on whether the latter is actually strong enough for league football. When Stevens went off, Kal Naismith replaced him which then meant the two centre backs were flanked by wingers rather than full backs. Not ideal, is it?
The defence shouldn't shoulder all of the blame, however, as there were enough chances to win the game in the first half alone but Chaplin missed the best of them. That might bring fans back to earth when describing him because whilst he is clearly talented, he is still learning.
He still found the net, though and that cannot be said of Main. He hasn't exactly made a name for himself since joining Pompey and people will be wondering what he actually brings to the team.
There are still many more questions that this result has forced Blues fans to ask but to ask them all now would see this article go on forever. With Plymouth winning and extending their lead over Pompey to eleven points, you may as well kiss the League Two title goodbye now.
But even if Argyle were to capitulate, there are too many problems at both ends of the pitch that need solving before Portsmouth can be considered serious candidates for automatic promotion.
Pompey Player Ratings
David Forde: 5 - Not the most confident showing.
Gareth Evans: 5 - Struggled with defending pace on the break.
Christian Burgess: 4 - Lacklustre and sluggish.
Tom Davies: 4 - Not strong enough.
Enda Stevens: 6 - Hopefully injury isn't too serious.
Michael Doyle: 5 - Doesn't look the same player as last season.
Amine Linganzi: 7 - A capable performer.
Gary Roberts: 6 - Has been too quiet in recent games.
Carl Baker: 6 - Lost his battle with the Magpies keeper.
Kyle Bennett: 7 - A livewire. Shouldn't have been taken off.
Conor Chaplin: 7 - Should have scored more than one.
Kal Naismith (Stevens 59):5 - Delivery was poor.
Milan Lalkovic (Bennett 74): N/A - Probably thinks he should be starting more often.
Curtis Main (Chaplin 70): N/A - Scuppered his one big chance.