At 2-0 after 79 minutes, the Blues looked out of it until substitute Reeco Hackett pulled one back and threatened to inspire a remarkable late comfortable.
However, in stoppage time, Plymouth hit the visitors on the break to seal their victory and a return to the top of the table, yet there were some positive Pompey performances.
Here are our on-the-whistle player ratings...
9. Ryan Tunnicliffe - 5
(Replaced by Reeco Hackett on 68 minutes) Found it tough in the middle and unable to affect Pompey positively with his passing. One awful second-half shot summed up his disappointing afternoon. Photo: National World
10. Joe Morrell - 6
(Replaced by Denver Hume on 85 minutes) Dogged and full of heart, but couldn’t influence the Blues as much as recent weeks. Plugged away, though, and he remains such a key performer. Photo: National World
11. Owen Dale - 5
(Replaced by Paddy Lane on 68 minutes) Frustratingly quiet and unable to get involved in proceedings, despite usual effort and commitment. There was a first-half shot straight at Callum Burton and a couple of useful crosses, but not enough. Photo: National World
12. Colby Bishop - 6
Led the line as he always does with effort and endeavour, just was never presented with that sniff of goal to add to his tally. Barely had a chance in a match when Pompey didn’t create enough, Photo: NationalWorld