Things could have been so different if Kevin-Prince Boateng had converted a penalty for Pompey but, after Petr Cech had saved the tame effort, Didier Drogba scored the only goal of the game when he guided a free-kick home less than three minutes later.
Frank Lampard missed a spot-kick of his own at the death but it still proved to be Chelsea's day as coach Carlo Ancelotti completed a memorable debut season in charge of the Londoners.
The Premier League champions started strongly and struck the woodwork no less than five times in the opening period.
Lampard was the first to go close inside four minutes when his drive from the edge of the area flew just wide of David James' post and, soon after, he went even closer to breaking the deadlock.
He picked the ball up from distance before unleashing a dipping, swerving effort and, with James beaten, his effort clipped the outside of the post before going behind.
Pompey almost grabbed an unlikely lead when Boateng's volley was deflected inside the six-yard box by Frederic Piquionne, but Cech was in the right place at the right time to turn the ball away.
Ashley Cole then turned Steve Finnan inside out before squaring to Salomon Kalou but, with the goal gaping, the Ivorian inexplicably hit the bar from close range.
John Terry was the next to come within a whisker of scoring when he planted a header against the bar from Florent Malouda's centre.
Drogba then went even closer to breaking the deadlock when his stunning free-kick was expertly tipped onto the underside of the bar by James before bouncing clear. He then hit the outside of the post after wriggling past the challenges of Finnan and Aaron Mokoena as the interval loomed.
Pompey were handed a superb chance to take the lead when substitute Juliano Belletti felled Aruna Dindane inside the penalty area but Boateng's half-hearted 55th-minute spot-kick was blocked by Cech's legs.
The near-miss stirred the Pensioners into action and just moments later they grabbed the lead.
Drogba broke free and, after Mokoena had brought him down, he fired the resulting free-kick in off the far post.
Chelsea looked more likely to double their lead and, with time running out, Lampard was brought down by Michael Brown and referee Chris Foy blew for another penalty.
Although the usually reliable midfielder screwed his spot-kick wide, it didn't prove costly as the Stamford Bridge outfit saw out the three minutes of stoppage time to clinch another FA Cup trophy in front of their jubilant followers.