The Latics seemed to be struggling when their hosts enjoyed the better of the opening half and took the lead at the start of the second period.
Simon Francis delivered a fantastic right-wing cross into the path of striker James Walker and he volleyed the ball into the back of the net from six yards for his first league goal of the season.
But Southend, who began the day just one place below Oldham, failed to build on the opener and they allowed the visitors back into the game.
Adam Federici had already done well to deny both Lee Hughes and Darren Byfield before Chris Taylor finally drew the visitors level with a near post header from Andy Liddell's right-wing corner in the 67th minute.
Oldham then made sure of the win when Hughes latched onto a Taylor free-kick to volley into the bottom left-hand corner of the net at the back post.
John Sheridan's side comfortably held on to the advantage and secured a winning return to Roots Hall for their midfielder Kevin Maher who spent ten seasons with Southend before being released last summer.