Charlton’s nine match unbeaten streak came to an end at Glanford Park on Saturday.
Two quick fire goals from substitute, Josh Morris, in the second-half won the game for Scunthorpe, and extended their winning run to six.
The Addicks played in their all white third kit for the first time this season, on a bitterly cold afternoon in North Lincolnshire.
Karl Robinson covered for the absence of Ben Reeves by playing Ricky Holmes in the middle, and pushing Jay Dasilva forward into the left hand side of midfield.
Patrick Bauer returned to partner Ezri Konsa in central defence, with Naby Sarr moving to the left to replace Dasilva.
It was a notable afternoon for skipper, Chris Solly, who made his 250th appearance for the club.
Holmes was at the heart of most of Charlton’s best attacking moments, and created the visitors’ best chance after 27 minutes.
His deep cross found Josh Magennis at the far post. But Matt Gilks managed to tip the Irishman’s header onto the post.
Graham Alexander brought Josh Morris on at the interval, and the winger was the catalyst that turned the game in Scunthorpe’s favour.
Two goals in two minutes just past the hour mark put the game beyond the Addicks’ reach.
First, he fired home a free-kick on the left hand side of the box, then two minutes later, he unleashed a thunderbolt that gave Ben Amos no chance.
Charlton were not at their best, but looked to be heading for at least a share of the spoils until game changing Morris entered the fray.
The Addicks play Peterborough in one of their games in hand at The Valley on Tuesday. Robinson will be desperate for his side to take all three points.
Charlton: Amos; Solly, Konsa, Bauer (Ahearne-Grant, 70), Sarr; Kashi, Forster-Caskey, Marshall (Hackett-Fairchild, 85), Holmes, Dasilva; Magennis
Subs (not used): Phillips, Dijksteel, Jackson, Aribo, Dodoo.
Booked: Konsa 90 (scuffle).
Scunthorpe: Gilks, Clarke (Holmes, 17), Burgess, McArdle, Wallace; Adelakun (Crofts 76), Bishop, Ojo, Lewis (Morris 46); Madden, Hopper.
Subs (not used): Watson, Townsend, van Veen, Goode.
Goals: Morris 61, 63.
Booked: Adelakun 69 (foul), Hopper 90 (scuffle).
Referee: Kevin Johnson (Weston-Super-Mare).
Attn: 4,307.