Hamer produced a number of fine saves as Scunthorpe hit back to dominate after falling behind to an early goal.
Looking to bounce back from two successive defeats, Charlton went ahead in the sixth minute when leading marksman Bradley Wright-Phillips netted his 20th goal of the season with a brilliant finish following Chris Solly's cross.
Rhoys Wiggins was at fault in the 20th minute when he brought down Scunthorpe striker Garry Thompson in the penalty area and Jon Parkin crashed home his fifth goal during his loan spell from Cardiff from the spot.
Scunthorpe, unbeaten in their previous four games, quickly grew into the game and nearly snatched the lead either side of half time, but Thompson and Andy Barcham were denied by Hamer.
Scunthorpe dominated much of the second half, with Hamer again rescuing the visitors with another full length save from Barcham, while Parkin wasted a golden chance in the 60th minute when he fired over from close range.