Carl Winchester's superb solo strike was the difference between the two sides as Latics picked up a vital three points at Glanford Park.
With only five minutes of the game remaining, the Northern-Irishman drove into the box and finished past the goalkeeper to win the game for Latics putting them into a play off place.
The game took a while to get going but it was the visitors that had the first opportunity of the game on 11 minutes.
Gary McSheffrey's inswinging free kick was headed into the path of Neal Bishop to shoot on the volley but it went past the post.
Latics started to grow into the game and Carl Winchester's through ball into the path of Forte on 15 minutes was just gobbled up by Iron goalkeeper Luke Daniels.
Timothee Dieng was next to go close for the visitors a minute later but he scuffed his shot wide from 25 yards.
Latics were in the ascendancy and needed to capitalise on their opponents vulnerability.
They nearly did that mid way through the half as top goalscorer Jonathan Forte received the ball on the edge of the box but scissor-kicked his effort over the bar.
Latics had to be wary on the break as full back Jordan Clarke crossed onto the head of Tom Hopper but the striker knocked it narrowly past the post.
The home side came back into the game but were struggling to force their way through a solid Athletic defence.
Ten minutes before the break came the best chance of the half and it fell for the visiting side.
Mike Jones' whipped free kick found the head of George Elokobi who knocked the ball back into the centre for the onrushing James Wilson but somehow the ball went past the post from five yards out.
Athletic finished the half positively and could have been awarded a penalty in additional time but the referee waved away Conor Wilkinson's protests.
Latics started the second half very brightly and had two chances to take the lead within the first five minutes.
Wilkinson rose highest from a Brian Wilson cross but Daniels saved comfortably. Only seconds later, Jones' corner found the head of Liam Kelly but it bounced over the crossbar.
Latics were all caught forward two minutes later. A long ball over the top found a way past Jake Kean but Joseph Mills recovered and cleared the danger.
The Iron did have the ball in the goal on 52 minutes but the linesman's flag prevented the home side taking the lead.
Just before the hour mark, Forte capitalised on a defensive error and raced through on goal but Daniels stood tall and denied the striker from extending his scoring record to 15.
Latics were in control of the game but could not find a way past a stubborn Daniels in the Iron goal.
Rhys Murphy made his Oldham Athletic debut, replacing Jones on 78 minutes and was straight into the action.
The striker fed Wilkinson through but his shot was tame and Daniels saved comfortably.
With both sides pressing, Latics did eventually take the lead five minutes from time through a superb individual strike from Winchester.
The midfielder picked up the ball midway through the Iron half, ran past two defenders and finished off the inside of the post to win the game for the visitors.
It was the Oldham Athletic fans you could hear in the stands and they comfortably saw the game out to pick up a vital three points as Latics moved into the play-off spots.
Scunthorpe United: Daniels, Clarke, Boyce, Canavan, Williams, Bishop, O'Neil (Evans 68'), Osbourne (Adelakun 90'), McSheffrey, Madden, Hopper (Van Veen 75').
Subs not used: Anyon, Nolan, Murphy, Davey.
Oldham Athletic: Kean, B.Wilson, J.Wilson, Elokobi, Mills, Dieng (Mellis 69'), Kelly, Jones (Murphy 78'), Winchester, Forte, Wilkinson (Poleon 85').
Subs not used: Coleman, Kusunga, Brown, Turner.
Goals: Scunthorpe United 0-1 Oldham Athletic (Winchester 84')
Attendance: 4,125 (609 visiting supporters)