Blues suffered back-to-back home defeats in League One after Ivan Toney’s late strike secured Peterborough a 3-2 win at Roots Hall.
Despite the number of players missing for Blues, they more than matched the league leaders in the first-half but were undone by a Siriki Dembele free-kick which was bundled in by Godden.
The Posh doubled their advantage early in the second-half, again from a set-piece, with Godden putting the finishing touch on the move by smashing it high into the roof of the net.
Southend’s Player of the Month for August, Tom Hopper, reduced the arrears after tapping in Simon Cox's cross from close range before Stephen McLaughlin fired Blues level with 15 minutes to go.
With both sides pressing for a winner, Peterborough caught the Blues late on after Joe Ward’s cross across the six-yard box was fired home from close range by Ivan Toney to win it.
The goal, in front of the Peterborough fans, had manager Steve Evans on the pitch celebrating with Peterborough picking up their first win at Roots Hall since 1999.
Victory for the visitors maintained their place at the top of the table while it was a disappointing way for Chris Powell to celebrate his 49th birthday with a third home defeat of the season.
It was yet another 87th-minute strike that cost Southend a point in a game where they more than matched up to the table-toppers despite Blues' ever-growing list of absentees.
Hours before the game, Southend confirmed the emergency loan signing of goalkeeper David Stockdale and he went straight into the starting line-up as one of four changes Chris Powell made from the league defeat to Charlton last weekend.
Southend’s visitors Peterborough arrived at Roots Hall brimming with confidence having won five and drawn one of their opening six league games, and they almost got off to the perfect start when Jason Cummings was picked out inside the area only to side-foot his effort just wide.
Blues knew they were in for a tough afternoon against the league leaders, but Chris Powell’s side more than held their own in the first-half and created a number of decent opportunities on the Posh goal.
Neat interplay down the right allowed Elvis Bwomono to get goal side and his near-post cross couldn’t be diverted on target by Tom Hopper, before Stephen McLaughlin forced a smart save from Aaron Chapman who sprung across to his right to save the Irishman’s free-kick.
But arguably against the run of play, Steve Evans’ side took the lead after Siriki Dembele was brought down. His subsequent free-kick was chested down into the path of Matt Godden by Jason Cummings, allowing Godden to sweep the ball in at the near post.
It was a poor goal for Blues to concede but they responded well to going a goal down and Simon Cox will feel he should have done better when Sam Mantom’s loose strike fell to the number 10 inside the area, but he couldn’t get the connection required to trouble Chapman.
Timothee Dieng’s well-struck volley on the edge of the area had to be palmed away by Chapman and the giant goalkeeper was called into action again late in the half tipping over a McLaughlin header just before the interval.
Blues will have felt hard-done-by to go into the break behind, but Peterborough looked to increase their advantage early in the second-half and went close when Jamie Walker’s free-kick came off the top of David Stockdale’s crossbar.
Peterborough did though double their advantage as Blues were undone again by a set-piece. Marcus Maddison’s free-kick into the area was deflected across goal by Ryan Tafazolli and thumped into the roof of the net by Godden to make it 2-0.
Peterborough looked like they were cruising to their first win at Roots Hall since 1999 but Southend responded by halving the deficit with just under half an hour remaining when Cox’s low cross was just about tapped home by Tom Hopper.
Hopper’s strike had lifted the Roots Hall crowd and Southend rose their game accordingly with Harry Bunn stinging the palms of Chapman before playing the ball back into the area only for Hopper to fail to connect with the ball from close range.
Southend continued to press and a long ball over the top allowed Dieng to get goal side only for some last-ditch defending from Rhys Bennett to prevent the Frenchman, before Hopper’s header on goal was unable to be diverted beyond Chapman by Cox.
With the pressure mounting on Posh, it felt like only a matter of time before Southend levelled and they did just that with 15 minutes remaining. Cox and Coker were having all sorts of joy down the left and Coker once again got in behind before picking out McLaughlin to fire home the equaliser.
Remarkably, Southend were now in with a shout of picking up three points but with the game opening up and becoming end-to-end, Blues fell victim to another late goal as Ivan Toney won it for the visitors to keep them top of the league table.
Joe Ward, on as a substitute just moments before, made a well-timed run to get into the area. His strike was saved by Stockdale but Toney, another sub, was on hand to fire the ball in from close range and spark wild celebrations in the away end and on the Posh bench.
Blues XI: Stockdale, Bwomono, Coker, Turner, Dieng, Hopper, Cox (Robinson 83’), McLaughlin (McCoulsky 89’), Mantom (C), Bunn, White. Subs Not Used: Bishop, Klass, Moore, Hendrie, Batlokwa
Peterborough United XI: Chapman, Naismith, Daniel, Woodyard (C), Tafazolli, Walker (Maddison 55’), O’Hara, Godden, Dembele (Ward 78’), Bennett, Cummings (Toney 70’). Subs Not Used: Tyler, Reed, Cooper, Yorwerth
Referee: Kevin Johnson
Assistants: Daniel Cook & Paul Yates
Fourth Official: Anthony Coggins
Southend United: Tom Hopper 63’, Stephen McLaughlin 75’
Peterborough United: Matt Godden 32’, 57’, Ivan Toney 87’
Southend United: None
Peterborough United: Jamie Walker 50’
Attendance: 6,551 (819 Away Fans)