Nile Ranger, Theo Robinson and an Anthony Wordsworth penalty secured 10-man Southend United the win, who had Ryan Leonard sent off on 70 minutes.
Manager John Sheridan made one change to the side which drew 1-1 with Sheffield United last weekend.
Ryan McLaughlin replaced the injured Brian Wilson at right back and it would be Latics who had the better opportunities in the first half.
However, it would be Connor Ripley who was the first goalkeeper to be tested on 10 minutes.
A corner into the box found the head of Nile Ranger but Ripley managed to save and hold on to the ball.
Latics started to frustrate their opponents and cause a lot of problems.
Tope Obadeyi had a shot saved by Christian Walton on 11 minutes, whilst two minutes later, superb skill in midfield from Ollie Banks saw him cross to Lee Erwin but he could only volley over from 18 yards.
Latics continued to pile forward and winger Chris Taylor almost gave Sheridan’s men the lead midway through the half.
Obadeyi laid the ball back to the winger who curled towards the far post but it fell the wrong side of the post.
Paul Green went close minutes later whilst Obadeyi volleyed wide with Latics well on top.
Southend were restricted to shots from distance. Stephen McLaughlin cut inside from the right for the home side on the half hour mark but fired wide of Ripley’s goal.
10 minutes before the break, Josh Law almost broke the deadlock. He received the ball 30 yards from goal and fired towards the far post but it went inches wide of Walton’s goal.
Latics continued to frustrate Southend United with Anthony Wordsworth and Simon Cox going into the book before the half time break.
Southend almost took the lead minutes after the interval as Ben Coker drove an effort past Ripley’s far post from the right hand side.
After an injury scare to McLaughlin, Obadeyi found space in the penalty area but he took too long before he was dispossessed.
The referee made himself unpopular with the home supporters with a succession of decisions going against Southend United.
He further enraged the home fans after he only awarded Banks a yellow card when he was adjudged to have fouled Cox, who had a clear run on goal.
Cox had a great opportunity to give the Shrimpers the lead minutes later he had acres of space in the box but volleyed over the stadium.
Southend United were reduced to 10 men on 70 minutes after Leonard’s reckless challenge on Fane was punished by the referee.
Fane won the ball in midfield but Leonard was in late and the referee had no hesitation in producing the red card.
However, it would be the home side who reacted well to the sending off and they took the lead on 75 minutes through Ranger.
Robinson held the ball up in the penalty area, crossed into the box and Ranger was there unmarked to stab home to opening goal of the game.
The momentum was with the home side and they doubled their lead three minutes later through Robinson.
The striker rose highest from a free kick into the box and headed into the corner to put Southend two goals ahead.
Latics continued to pile forward in a bid to get something from the game as Erwin and Banks both had efforts on goal but they did not trouble Walton.
In the final minute of six minutes added time, the referee awarded Southend United a spot kick after Peter Clarke was adjudged to have fouled Jermaine McGlashen in the box.
Wordsworth stepped up and sent Ripley the wrong way to win the game for the home side.
Southend United: Walton, Coker, Wordsworth, Thompson, Cox (Timlin 73’), McLaughlin (McGlashan 54’), Atkinson (Robinson 64’), Leonard, Demetriou, Ferdinand, Ranger.
Subs not used: White, Fortune, Amos, Inniss.
Oldham Athletic: Ripley, McLaughlin, Clarke, Gerrard, Law, Green, Fane, Banks, Taylor, Erwin, Obadeyi.
Subs not used: Kettings, O’Neill, Flynn, Croft, Ngoo, Edmundson, Mantack.
Goals: Southend United (Ranger 75’, Robinson 78’, Wordsworth 90+6’) 3-0 Oldham Athletic
Attendance: 7,617 (285 visiting supporters)