The decision announced on Thursday by the Federal Department for Media Harmful to Young Persons (BPjM) means that the game can be bought by anyone over the age of 16.
"Doom" was placed on an index of media considered harmful to young people on its release in Germany in 1994, because of its extreme violence, which included depictions of various fantastical beasts being shot to death.
This meant that, like pornography, it could only be sold to adults in specialist shops.
According to Der Spiegel magazine, the BPjM originally called the game voyeuristic and sadistic.
Many gamers imported "Doom" from overseas, a common practice in Germany, where authorities consistently censor games because of their concern over violence.
The BPjM's change of heart was prompted by an appeal from the makers of Doom ten years after a final rating decision - the earliest legal opportunity. After 25 years, the rating will automatically be removed.
The BPjM has now acknowledged that scenes of violence in the game cannot be viewed as “realistic” by today's standards. The sequel "Doom II - Hell on Earth" has also been taken off the index.
But similar games such as "Wolfenstein 3D" remain on the government's banned list for the time being.
The success of "Doom" jump-started the first-person shooter genre, and its popularity led to a number of similar games, including “Quake” and “Duke Nukem 3D.”