Antonio German and Chris Whelpdale netted in each half with Jason Banton scoring for the visitors as Martin Allen’s side claimed another vital three points in their push for promotion.
They are now five points clear of Port Vale, who have taken just one point from the last four games following a 2-1 defeat by play-offs chasing Southend.
Vale's lack of confidence was obvious in the disjointed opening stages and Darren Purse came to the rescue after a mistake by Liam Chilvers let in Britt Assombalonga.
But Purse was culpable when his trip on Matt Lund, on loan at Southend from Vale's neighbours Stoke, led to the visitors taking the lead from a 19th minute penalty.
Sean Clohessy made no mistake with an unstoppable spot-kick high inside Chris Neal's left-hand post.
Assombalonga threatened twice more against a ponderous Vale defence before extending Southend's advantage in the 31st minute.
The fleet-footed striker turned Purse with ease and struck a right-foot shot from 14 yards which took a big deflection off Anthony Griffith to leave Chris Neal without a hope.
Lee Hughes gave the home side a lifeline just a minute later.
Chris Shuker flighted over a cross from the right and Hughes' glancing header from 10 yards sent the ball just inside Paul Smith's right-hand post.
Smith later denied Hughes an equaliser with a fine save, but Southend held firm for a deserved victory.
Torquay slipped closer to the relegation zone as they went down 3-1 at home to Oxford.
James Constable and a Damian Batt penalty put the visitors 2-0 up. Aaron Downes gave Torquay hope but Simon Heslop's late strike sealed the win.
Accrington could not take advantage of Torquay's defeat as goals from Chris Hackett and Roy O'Donovan saw them beaten 2-0 at fourth-placed Northampton.
Ten-man Rotherham slipped to sixth after a 2-1 defeat at home to Dagenham and Redbridge.
The home side had Kari Arnason sent off after bringing down Medy Elito in the area, and the Congolese midfielder picked himself up to open the scoring from the penalty spot. Claude Davis pulled the Millers level but Luke Wilkinson grabbed the winner eight minutes from time.
George Donnelly's late double helped Rochdale to a 4-1 win over Wycombe. Stuart Lewis had put Wanderers' ahead but an Ian Henderson strike and Michael Harriman's own goal saw the home side hit back before Donnelly sealed the win.
Fleetwood and Exeter played out a goalless draw while James O'Shea and Armand Gnanduillet gave Chesterfield a 2-0 success over Bristol Rovers.
Substitute Alan Connell scored a last-gasp penalty to earn Bradford a 1-1 draw against Aldershot, Kieron Cadogan had put the visitors ahead at the end of the first half.
Barnet hammered 10-man Morecambe 4-1 thanks to a Daniel Lopez hat-trick after the visitors had goalkeeper Barry Roche sent off. Jack Redshaw put Morecambe ahead but Luke Gambin levelled and Lopez's first made it 2-1.
Roche then brought down Gambin in the area and saw red, with Lopez converting the resulting penalty before completing his treble to improve the home side's survival prospects.
AFC Wimbledon hauled themselves out of the relegation zone as they emerged 3-2 winners over York, condemning visiting manager Nigel Worthington to a losing start.
Mat Mitchel-King put the Dons ahead but Chris Smith quickly headed in an equaliser. Brennan Dickenson put Wimbledon back ahead, only for Smith to level for a second time. But Harry Pell got the clinching goal with 11 minutes remaining.