Cowdery saved from both Copnor's Neil Bradley and captain Oliver Warren - after Danny Hayter had fired his spot-kick over the crossbar - as Southsea lifted the PDFA Trophy prize with a 3-0 shoot-out victory.
Jon Kercher, Joe Crowe and Taylor Kneller all kept their cool from 12 yards when it really mattered - yet United must have been wondering how it got to that point.
In a final that had it all, Southsea squandered a 3-0 half-time advantage to eventually draw 3-3 in normal time - they also missed a penalty - before running out shootout winners.
United blew away their City of Portsmouth Sunday League Division 4 rivals in the opening 45 minutes and must have been thinking the Trophy was already in their possession at the break.
Horndean-bound strike sensation Zak Willett, who'd scored an incredible 80 goals in 36 appearances for Southsea and Hampshire Premier League Paulsgrove heading into the final, turned provider as United took the lead.
The pacy forward picked up the ball and squared for Kercher to roll home from close range and hand Southsea the advantage on nine minutes.
Willett then notched goal number 81 of a stellar campaign just before the half-hour mark. Captain Fred Goldring's pass sent him clear and he had no trouble slotting past Luke Oldfield.
Southsea added a third six minutes before half-time. Willett was involved again, exchanging passes with Crowe, then setting up Jack Mulholland whose fierce drive from the edge of the area found the bottom corner.
Copnor looked down and out at the break, yet two goals in as many minutes just before the hour mark gave them some much-needed inspiration.
Top scorer Brad Hartill made it 3-1 with his 32nd goal of the season on 56 minutes then, less than a minute later, Copnor were handed another boost as Josh Bailey fired home.
Willett missed a penalty soon after for United, slotting his attempt from 12 yards wide of the post, as they missed the chance to restore their two-goal advantage.
Southsea were now shaken and Bailey completed a remarkable turnaround, cleverly finding the top corner on the turn with 22 minutes still remaining.
Copnor could easily have won it in normal time, but both Danny Hayter and Bailey, who was on a hat-trick, squandered glorious chances in the closing stages.
So it was a shootout to decide an enthralling final - and Cowdery proved the hero.
Southsea's Kercher, Crowe and Kneller all scored but after Hayter hammered his side's first spot-kick over the bar, Cowdery saved from Bradley and Warren as United lifted the silverware.
Southsea United: Cowdery; Kneller, SImpson, Crowe, Gleeson, Goldring, Camburn, Blackman, Mulholland, Willett, Kercher. Subs: Robertson, Betts, Granger.
AC Copnor: Oldfield; Gaudion, Warren, Lorenz, Bradley, J.Hayter, Moyo, D.Hayter, Connell, Rowe, Hartill. Subs: J.Simmons, M.Simmons, Sutherland.