Both sides created decent openings in a stop-start first half and Nile Ranger blazed a controversial penalty high over the bar.
Pitman was not so profligate, however, and his effort ensured the Blues claimed a second successive League One victory.
Kenny Jackett stuck with the same side that dramatically won at Blackpool the previous week.
That meant Oliver Hawkins continued to be used as a makeshift centre-back, with Matt Clarke playing on the left.
Nathan Thompson and former Shrimpers midfielder Stuart O’Keefe both had to be content with a place on the bench after returning from suspension.
With it being Pompey’s closest home match to Armistice Day, Normandy veteran John Jenkins MBE read the Ode of Remembrance before kick-off.
A bugler then played the Last Post before everyone inside Fratton Park observed a minute of silence.
The Blues came flying out of the traps and almost broke the deadlock inside the opening five minutes.
Clarke sent a superb cross into the box from wide on the left, but Pitman could not quite steer the ball on target from close range.
Anton Ferdinand then had to hack clear when a deep Ben Close free-kick was headed into the mixer by Christian Burgess.
The hosts were looking dangerous going forward and John White was forced to head behind at the far post when Jamal Lowe centred.
But Southend settled and enjoyed their own spell of pressure midway through the first half, with Luke McGee diving to keep out a snap-shot from former Pompey trialist Theo Robinson.
Kal Naismith then inadvertently diverted the resulting corner into Ranger’s path, although the striker could only fire wide.
It was a contest that offered flurries of excitement in the middle of long spells when the action lulled.
Kyle Bennett almost bagged a rare headed goal when he managed to rise highest in the box to meet Lowe’s delivery, only for Michael Turner to clear off the line.
Shrimpers keeper Mark Oxley was then forced to get down quickly in order to keep out a fierce drive from Close.
There were more half chances at both ends of the pitch before the game controversially exploded into life just before the break.
First Danny Rose and then Clarke bravely threw themselves into the path of shots to protect McGee’s goal.
But the linesman was waving his flag furiously on the sidelines and told referee Carl Boyeson that a hand had been used by Clarke.
The hosts were furious with the decision and Burgess led the protests – backed, of course, by the Fratton faithful.
But it mattered not, as the wasteful Ranger stepped up to take the penalty and blasted it high over the bar.
Southend United 0
Bennett did not emerge from the tunnel at the start of the second half, with Matty Kennedy brought on to replace him.
And it was the newcomer who provided the assist as Pompey broke the deadlock on 54 minutes.
He used his right foot to deliver a pin-point cross from wide on the left and PITMAN rose to expertly guide the ball into the net.
Fratton Park was then united in a minute of applause just before the hour mark to honour Blues fan Gary Martin, who recently passed away at the age of 58.
Pitman’s 12th goal of the season had been the only real moment of action in an otherwise slow start to the second half.
But a quiet spell ended when Cox’s shot was blocked by a well-placed Hawkins, with Gareth Evans getting the ball to safety.
Pompey were still looking a threat at other end, although Kennedy’s shot was not powerful enough to trouble Oxley.
Lowe then played a poor pass behind Pitman after being picked out on the right by Naismith’s threaded pass.
Southend tried their best to find an equaliser as they brought more men forward in the closing stages, but the Blues comfortably held on for victory.
Pompey (4-2-3-1): McGee; Evans, Hawkins, Burgess, Clarke; Close, Rose; Lowe (Thompson 87), Bennett (Kennedy 46), Naismith; Pitman (c)
Goals: Pitman 54
Subs not used: Bass, Donohue, O’Keefe, Chaplin, Main
Southend (4-1-2-1-2): Oxley; White (McGlashan 82), Turner, Ferdinand (c), Timlin; Leonard; Wright, Kightly; Cox; Robinson (Fortune 77), Ranger (McLaughlin 64)
Subs not used: Bishop, Hendrie, Bwomono, Yearwood
Referee: Carl Boyeson
Attendance: 18,431 (1,422 away fans)