On Friday afternoon newspaper expressen revealed the bomb scare at Liljeholmen on Wednesday was due to real and potentially lethal explosives.
Now Stockholm police's southern district confirms to news agency TT a 43-year-old man is held, based on overwhelming technical evidence.
He is charged with conspiracy to endangering the public through major criminal damage.
Expressen has cited anonymous sources saying the suspect was been traced from DNA traces on a coffee cup.
The intelligence service Säpo confirmed to the paper there was explosive material, but that there was no risk of detonation.
The police say they do not think the crime is connected to terrorism.
On Wednesday evening the café owner discovered the package, and the Liljeholmen shopping centre was evacuated.
By midnight the bomb squad was able to make the area safe.