Sheffield Wednesday striker, Clarke, had a long spell with Oldham last term, but he is now making a key difference to Southend and has netted twice in two games.
The visitors defended superbly after taking a first-half lead and were rewarded for their hard work despite having Garry Richards sent off just before the break.
Richards was shown a hotly disputed straight red card after hacking down Craig Davies with a late tackle from behind.
Southend were furious with the decision taken by referee Trevor Kettle, who angered both sets of fans with an inconsistent performance.
But Steve Tilson's side overcame their problems to inflict a fourth successive league defeat on misfiring Oldham.
Southend should have taken the lead after only four minutes as Alan McCormack crossed accurately from the left and Clarke could only steer his close-range header before the far post.
Oldham went close as Davies saw his cross-cum-shot cleared off the line and Southend keeper Steve Collis grabbed a header from Lee Hughes.
The breakthrough came on 28 minutes as Clarke chased down a flick-on and smashed his shot past keeper Mark Crossley from eight yards.
Oldham hit back as debutant Reuben Hazell missed the target with a header and winger Chris Taylor blazed over the bar from 12 yards.
The dismissal of Richards served only to steel the visitors and Oldham pounded away without making much of an impression on their solid defence.
Substitute Neil Eardley was denied by the woodwork when he let fly from well outside the box, but Southend were still relatively comfortable and the only threats of the last ten minutes came when Matt Wolfenden fired a good effort just over the top and former Southend striker, Michael Ricketts, hit a free-kick into the arms of Collis.