Andy Liddell's second half penalty was enough to end Northampton's unbeaten home record as 10-man Oldham clinched victory at Sixfields.
The striker sent goalkeeper Frank Fielding the wrong way from the spot, after Lee Hughes was fouled in the box.
Hughes twice had the ball in the net but both goals were ruled for offside, while he also hit the post.
The visitors ended the game a man down after Hughes picked up a second booking in stoppage time.
Northampton: Fielding, Crowe, Kyle Walker, Dolman (Guttridge 70), Hughes, Holt, Jackman, Dyer (Bignall 56), Gilligan, Constantine, Hawley (McGleish 56). Subs Not Used: Dunn, Davis.
Oldham: Crossley, Lomax, Hazell, Stam, Jones, Smalley (Liddell 8), Allott, Maher, Taylor, Hughes, Byfield, Liddell (Gregan 90). Subs Not Used: Eardley, Fleming, Alessandra.
Sent Off: Hughes (90).
Booked: Hughes, Byfield.
Goals: Liddell 76 pen.
Att: 5,067
Ref: Paul Taylor (Hertfordshire).
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