The result moves Rovers top of League One after Leyton Orient, who were three points above Tranmere, were hammered 5-0 at home by Swansea City, meaning Rovers moved ahead of The O's on goal-difference.
Ronnie Moore made two changes to the side that drew with Crewe in midweek, as Carl Tremarco replaced Mike Jones in midfield whilst more worryingly, Chris Greenacre didn't play after collapsing with a viral infection, meaning Antony Kay started in midfield and Taylor upfront alone in a 4-5-1 formation.
Southend looked to put the pressure on the away side early on, but neither Gower nor Barrett could test the 'keeper with their efforts in the first four minutes, whilst down the other end on six minutes Steven Jennings' 35 yard shot also drifted wide.
A well worked free-kick routine almost brought the first goal of the game for Tranmere though soon after, as Shane Sherriff once again drifted un-noticed and un-marked to the far post where he was found by Paul McLaren. The Australian shot but saw 'keeper Collis pull off a fine save at his near post.
John Achterberg was called into action on 12 minutes as he saved Odhiambo's shot as the striker used his pace to break clear of the defence. However, Achterberg was equal to the strikers' efforts, diving down low to palm the ball away.
Down the other end, Shuker was the latest Tranmere played to try a shot from distance but again the winger failed to work the 'keeper.
On 30-minutes, Tranmere took the lead through the most unlikely of goal scorers, Ben Chorley, the defending netting his first for the club.
After a magnificent passing move which had seen Rovers work the ball across the back, midfield and attack and seen them retain possession for what must have been close to 40 passes, Rovers won a corner. Paul McLaren took the set-piece, sending the ball towards the near post where it was met by Chorley, the defending carressing a wonderful half-volley into the bottom corner.
But, with little action for the next 43 minutes, Southend equalised through Adam Barrett, who according to the matchday program is very close friends with Rovers striker Chris Greenacre.
Chorley sliced a clearance towards the Rovers right where it was picked up by a Southend played. The ball was quickly worked over to the left where Hunt, un marked due to the strange absense of Shane Sherriff, crossed to Barrett who vollied in through a crowd of players, leaving Achterberg no chance as he dived to his left.
Half time came then, and the stadium announcer brought some good news for both sets of fans. Not only were Leyton Orient already 2-0 down to Swansea, but England had shocked the rugby world with a 12-10 win over Australia in France. Adding to Southend's new found joy was the fact that Colchester United were losing 1-0.
Southend came close to taking the lead not long after the re-start as John Achterberg made another splendid save in the Tranmere goal, tipping Garry Richards' header onto the bar and away from goal for a corner before Tranmere took the lead again on 55-minutes.
Tranmere were awarded a free-kick near their right hand touchline for a foul on Shuker, and Paul McLaren stepped up to take the set-piece. It was another immaculate delivery from the Tranmere number four, as he found Taylor who sent a bullet header past Collis and into the goal in front of the travelling fans who went absolutely barmy.
If they heald on, Tranmere would now finish top of the league, but it was to be an anxious final 35 minutes for all involved with the club.
The Super Whites pushed for a third, as first Taylor came close again before a slip up in midfield by Southend allowed Carl Tremarco to carry the ball forward from the half-way line and shoot from around 25-yards, forcing Collis into another great save as he dived to his right.
The action was back down the other end soon though as Southend had around ten minutes of constant play in the Rovers half as they pushed for a goal.
Nick Bailey first forced Achterberg into a save as the Dutchman deflected the ball out for a corner before the 'keeper parried an effort from Gower soon after.
On 67 minutes, Tranmere made the first change of the game as young striker Craig Curran replaced the tired Chris Shuker on the right-wing as Rovers looked to add some pace as well as a pair of fresh legs to the field.
However, eight minutes later it was Southend's turn to ask the questions of Ronnie Moore as Steve Tilson made a triple substitution, bringing Harrold, Foran and Black on for Gower, McCormack and Odhiambo.
Southend put on the pressure again as they won a string of corners, but the best chance swere coming at the other end as Collis was forced to tip Sherriff's 25-yard free-kick over the bar after Curran had been fouled on the left-hand side of the box.
The resulting corner brought a controversial moment though, as McLaren's (eventual) cross found Goodison and his as he bundled the ball towards goal, if definately appeared to cross the goal line but no goal was given. Protests from Stockdale, Goodison, Taylor and McLaren in particular seemed to suggest that the ball had indeed crossed the line and the Tranmere fans, who were at that end of the ground, knew it had too.
On 84-minutes, the once again brilliant Gareth Taylor (something we are getting used to now), was replaced by Calvin Zola upfront as the striker made his return from a hamstring injury.
Southend continued to throw the ball forward and it at the Tranmere end it looked as if one shot had hit the bar when in fact it had hit the stansion behind the goal and gone out of play for a Tranmere goalkick.
All their pressure was to no avail, as Tranmre claimed a deserved and vital win to move top of Coca-Cola League One for the first time after a ful fixture list.
The team performance was absolutely brilliant and there was not one player who didn't put in a good performance.
The travelling Tranmere fans were once again superb. Just over 300 of them were in the allocated away section and they generated the noise of 1000 fans as they sang all afternoon and the players showed their delight after the match as they came and clapped the fans who in turn gave the players a standing ovation.
Jones' Man Of The Match: With so many good performances, it is hard to pick one player as man of the match. However, Taylor was again magnificent whilst Tremarco and Stockdale too were superb. The outstanding man of the match however for me was Steve Jennings, who was once again increadible in the midfield, showing so much energy and winning so many tackles as he helped Rovers to victory.