It was Die Nationalelf's first defeat in 17 outings and forced them to fall short of their pre-tournament expectations.
Germany opened the scoring in the 16th minute when Magull flicked an incisive Sara Dabritz pass up to waist height before swiveling on her left foot and firing home with the right to beat a helpless Hedvig Lindahl.
Sweden leveled six minutes later on a stellar run from Jakobsson, who was the beneficiary of a probing long-ball clearance from central defender Linda Sembrant. It was a horrible defensive miscue for a Germany side that had not conceded a goal in the tournament prior to Saturday.
Blackstenius doubled Sweden's lead three minutes after the interval when she was the recipient of a fortuitous rebound that the striker slotted home with relative ease.
For just the third time in World Cup history, two-time winner Germany will not be present at the semifinal stage. Nor will it compete at the Olympics, as Martina Voss-Tecklenburg's lot missed out on one of three qualifying spots for European sides.
Sweden, a 2003 finalist, will now face the Netherlands in Lyon on July 3 with a trip to the tournament showpiece on the line.