Italy's anti-doping agency issued the verdict for the retired swimmer on Tuesday, and gave the same sentence to Magnini's relay teammate, Michele Santucci.
The swimmers were linked to nutritionist Guido Porcellini, who was banned for 30 years for distributing illegal drugs.
Magnini, who won the 100-meter freestyle at the 2005 and 2007 world championships and a relay bronze at the 2004 Olympics, has never tested positive and maintains that he never doped. He was an outspoken critic of doping throughout his career, having taken part in an "I am doping free" initiative.
Santucci teamed with Magnini when Italy won bronze in the 4x100-meter relay at the 2015 worlds.