Late New Year's Day heartache for Blues
A stoppage-time strike from Ryan Leonard ensured Pompey got 2014 off to a miserable start.
The visitors dominated the first half and deservedly took the lead when Sonny Bradley converted a corner.
But Leonard levelled just before the break and then broke Blues hearts with a sensational winner at the death.
Richie Barker made four changes from the side that drew with Northampton on Sunday.
Bondz N’Gala returned in central defence, while Jack Whatmough was handed a central midfield role.
David Connolly wore the captain’s armband up, with Ryan Bird playing wide on the right on a 4-2-3-1 formation.
Johnny Ertl, Romain Padovani and Patrick Agyemang all dropped to the bench, while Danny East missed out with a hamstring injury.
It was the visitors who were first to threaten, although Ricky Holmes’ low drive was straight at Southend keeper Daniel Bentley.
The hosts’ had their opening opportunity on eight minutes when Michael Timlin curled wide from distance.
But the Blues had started brightly and Bentley was forced to tip Marcos Painter’s free-kick over the bar after Holmes had won a free-kick out wide.
And the keeper was called into action again on 15 minutes, getting down low to his left to brilliantly deny Holmes, who had met Jed Wallace’s precise cross.
Southend broke quickly from the resulting corner, however, and Leonard’s drive had to be parried away by Trevor Carson.
The visitors received a blow on 20 minutes when Holmes – who had suffered a blow to the head a few minutes earlier – was forced to limp off injured and be replaced by Ashley Harris
But Pompey were soon back on the attack and Wallace cut inside before forcing another save from Bentley, while the following corner saw Bondz N’Gala have a header blocked.
And the pressure paid off on 29 minutes when Harris swung a corner into the box and BRADLEY arrived to side-foot home his first first Blues goal.
Southend did not look like a side in the promotion hunt as they struggled to keep hold of the ball.
Bentley was single-handedly keeping them in the game and was at it again on 37 minutes to deny Wallace, while Bradley then fired over from the resulting corner.
Southend did then have a chance to level after breaking quickly, but Carson comfortably kept out Cauley Woodrow’s curling strike.
But the hosts did equalise late in the first half, with Leonard’s effort catching a deflection to take the ball past Carson.
There was still time for Pompey to try to hit back before the interval, though, and Thery Racon curled a shot inches past the post.
Half Time: Southend 1 Pompey 1
With the wind now working in their favour, Southend unsurprisingly looked the more dangerous attacking side at the start of the second half.
Carson was being well protected by his back four, although he did have to keep out Barry Corr’s cleanly-struck effort on 59 minutes.
The conditions then almost helped Southend take the lead, with Kevan Hurst’s corner catching a strong gust and curling onto the roof of the net.
Pompey had not looked too threatening, but they did go close on 67 minutes when Racon cut the ball back and Harris fired just over.
Barker then made his second substitution moments later, with Agyemang replacing the tiring Connolly up front.
But it was Joe Devera who should have put the Blues back in the lead 70 minutes, only to clear the crossbar from close range after exchanging passes with Agyemang.
And Wallace continued his incredible streak of hitting the woodwork when he curled a superb strike against the crossbar.
Racon then tested Bentley’s handling in the wet conditions, with a drive from distance that the keeper gathered at the second attempt.
Instead it was the hosts who grabbed a stoppage-time winner when Corr knocked the ball down for Leonard to slam home from 25 yards.
Southend (4-3-2-1): Bentley; White (c), Phillips, Prosser, Coker; Atkinson (Clifford 82), Leonard, Timlin; Hurst, Straker (Corr 40); Woodrow (Eastwood 68)
Goals: Leonard 45, 90+2
Subs not used: Smith, Thompson, Laird, Payne
Pompey (4-2-3-1): Carson; Devera, N’Gala, Bradley, Painter; Racon, Whatmough; Bird, Holmes (Harris 20 (Padovani 82)), Wallace; Connolly (c) (Agyemang 69)
Goals: Bradley 29
Subs not used: Sullivan, Maloney, Ertl, Awford
Referee: David Phillips
Attendance: 7,736 (998 Pompey fans)