Haughton saved from Southampton Women's Shannon Sievwright and Georgie Freeland in the shoot-out as Jay Sadler's side ran out 3-2 victors and lifted the silverware for the 12th consecutive season in front of supporters at Westleigh Park.
Katie James, Mia Adaway and Danielle Rowe were all on the mark from the spot for Pompey, before opposition goalkeeper Kayla Rendell smashed her penalty against the crossbar.
Pompey Women had been pegged back in normal time as it finished 1-1, with penalties needed to decide the final.
Skipper Jade Bradley's stunning first half free-kick was cancelled out by Rachel Panting's strike after the restart prior to Pompey coming through on penalties.
Captain Bradley fired Pompey ahead with a fine curling free-kick from a tight angle towards the right edge of the area after 11 minutes.
But it was Southampton who had settled the better and looked more assured in the early exchanges.
Pompey defender Jaz Younger superbly cleared Rachel Panting's goalbound header off the line following Ella Morris' brilliant marauding run and cross down the right on 20 minutes.
But it was the Blues who could have doubled their lead 10 minutes before the break. Milly Mott's loose pass went straight to Jade Widdows, who could only fire straight at goalkeeper Kayla Rendell from just inside the area.
Southampton pulled themselves level 12 minutes after the restart as Panting's drilled effort found the bottom corner.
Younger came close to restoring Pompey's lead but her flicked header from Bradley's free-kick was parried away by Rendell, with Rebekah Tonks' effort on the rebound blocked.
The Blues had goalkeeper Hannah Haughton to thank for keeping them level 17 minutes from time. First, Danielle Rowe blocked Phoebe Williams' sweetly struck volley before Pusey had an effort brilliantly saved by the Pompey stopper.
Haughton again came to Pompey’s rescue deep into stoppage-time, gathering Williams’ flicked header as it went to penalties.
It would be Haughton who then starred in the shoot-out, saving two penalties to ensure the Blues secured a 3-2 shoot-out triumph.