Oldham notched their first victory of the season thanks to Matt Smith's winner at Scunthorpe.
Substitute Smith sealed the win for the Latics when he headed home Filipe Morais' free-kick.
David Mellor had given the visitors an early lead from James Wesolowski's pass before Chris Dagnall levelled with a superb individual effort.
Visiting defender Jean-Yves Mvoto was sent off in injury time but the Iron were unable to capitalise.
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Oldham Athletic manager Paul Dickov told BBC Radio Manchester:
"(The win) was very important as the one thing I didn't want to do after the first two league games was panic.
"I don't leave players out easily but I felt after Saturday we needed to go back to basics and be more solid.
"The one thing I will say about the boys I left out was their attitude was fantastic."