It dented the promotion challenge of a Charlton side, who arrived at Glanford Park boasting the best away record in the division with only three previous defeats on their travels.
But the Londoners were sunk by a battling Scunthorpe side, who finished the game with ten men after having central defender Andy Butler sent off in the 75th minute for a second bookable offence.
United were inspired by the arrival of new loan signing Geoff Horsfield.
The veteran targetman gave a robust display to unsettle the visitors defence.
He could also have had a couple of goals but rustiness showed in his finishing as he headed a good chance wide of the target in each half.
The only goal of the game came in the 63rd minute when Scunthorpe's leading marksman Martin Paterson came off the bench to net his 12th goal of the season.
He pounced from close range after a blunder by Charlton defender Yassin Moutaouakil.
Minutes earlier the same Moutaouakil also blundered at the opposite end when he shot wide from inside the box with the Scunthorpe defence all at sea.
Charlton looked a classy outfit with skipper Matt Holland pulling the strings in the middle of the park.
But for all their possession they struggled to create much in front of goal.
They were out of luck early in the second half when recent signing Andy Gray forced the ball home from close range only to be flagged offside.
And Charlton should have done better in stoppage time when substitute Izale McLeod could have salvaged them a point when he lifted his shot over the bar after goalkeeper Joe Murphy had done well to save from Chris Iwelumo
Scunthorpe have now taken four points this season from the Londoners and manager Nigel Adkins will be hoping he can use this result as a turning point to lift his side clear of relegation trouble after only their second win in 18 games.