But the visitors were in no mood to celebrate after throwing away a three-goal advantage at Roots Hall.
Bryn Morris, Ben Close – on his 100th appearance for the club – and Oli Hawkins all found the target as the Blues cruised into a commanding advantage.
Simon Cox reduced the deficit before the break, however, then added a penalty before completing his treble late on.
Kenny Jackett made three changes from the side that drew at Plymouth the previous weekend.
Viv Solomon-Otabor was handed his debut wide on the left, while Hawkins and Anton Walkes both returned to the starting line-up.
That meant a switch to a 4-4-2 system with Hawkins partnering Omar Bogle, as Matt Clarke claimed the captain’s armband.
Gareth Evans and Ronan Curtis both dropped the bench, while Nathan Thompson missed out with a knock.
There was a minute’s applause ahead of kick-off in memory of World Cup-winning goalkeeper Gordon Banks, who passed away earlier in the week.
It was the hosts who had the first effort, but Craig MacGillivray got down to his right to keep out Stephen McLaughlin’s low drive.
Christian Burgess then cleared the danger before Michael Turner could capitalise after Cox’s initial effort had been blocked.
But the Blues soon took control and broke the deadlock on eight minutes, as MORRIS opened his account for the club.
Bogle and Jamal Lowe combined well down the right and when the latter’s cross was pushed out by Nathan Bishop, the midfielder hammered the loose ball into the roof of the net.
They came close to doubling the lead from a corner soon after, with Clarke’s shot blocked and Burgess’ follow-up nervously dealt with by Bishop.
The visitors were well on top, although MacGillivray spilled an effort from Sam Mantom and dived on the loose ball before Michael Kightly could pounce.
And Pompey immediately went up the other end to strengthen their advantage, although the Shrimpers could have dealt with it.
Solomon-Otabor combined well with Lowe, but first Sam Hart and then Mantom made a hash of their clearances and CLOSE sent a neat volley into the bottom corner from the edge of the box.
It looked like they had gone even further ahead when Bogle managed to force the ball over the line, although it was controversially ruled out for offside.
But they did have a third goal on 31 minutes when, at the end of a neat passing move, Morris struck the post.
This time it was Taylor Moore’s chance to decline the opportunity to clear the ball and a grateful HAWKINS slotted home.
Southend looked out of the contest, but gave themselves a lifeline when Cox rose in the box to convert Hart’s delivery.
They almost grabbed another before the break when a corner fell for Turner, who curled his shot just past the post.
Southend United 1
The visitors began the second period brightly and a snap-shot from Bogle was saved by Bishop, while a heavy first touch from Lowe allowed the Southend keeper to claim the ball.
But Burgess then made a key challenge inside the box to stop Kightly collecting MacLaughlin’s pass following a quick break.
Pompey immediately created an opening of their own, but Bishop kept out Bogle’s effort and then beat the striker to the loose ball.
It was not as action-packed since the restart, however, and the chances started to dry up as the half progressed.
McLaughlin did try his luck from outside the box, but the ball struck Clarke to divert it wide of the post.
A couple of corners for the hosts also caused problems, although MacGillivray was on hand to deal with them on each occasion.
Solomon-Otabor had faded slightly following a lively start to the contest and was replaced by Curtis on 71 minutes.
And Jackett soon made a second substitution, with Bogle the man to make way as Evans provided fresh legs to the forward line.
The game seemed to be drifting towards a conclusion, but Southend were not done yet and set up a tense finale by pulling another goal back.
Morris caught Kightly in the box and referee Dean Whitestone pointed to the spot, with Cox stepping up to send MacGillivray the wrong way.
Pompey were not just sitting back, though, and Close had a low effort blocked following some patient build-up play.
But Southend completed a remarkable comeback on 88 minutes, as Cox raced onto Timothee Dieng’s fine pass and neatly tucked away his hat-trick goal.
James Vaughan was brought on as the Blues tried to hit back, but they were unable to find another goal before the final whistle blew.
Southend (4-4-2): Bishop; Bwomono, Turner, Moore, Hart; McLaughlin, Mantom (c) (Hutchinson 73), Dieng, Kightly (Wabo 82); Cox, Humphrys (Klass 25)
Goals: Cox 36, 78 (pen), 87
Booked: Klass, Moore
Subs not used: Smith, Kiernan, Lennon, Kelman
Pompey (4-4-2): MacGillivray; Walkes, Burgess, Clarke (c), Brown; Lowe (Vaughan 88), Morris, Close, Solomon-Otabor (Curtis 71); Hawkins, Bogle (Evans 75)
Goals: Morris 8, Close 20, Hawkins 31
Booked: Walkes, Vaughan
Subs not used: Bass, Casey, Haunstrup, May
Referee: Dean Whitestone
Attendance: 7,300 (1,239 Pompey fans)