The 29-year-old Brazilian striker scored over 100 goals in the J-League top flight, and will now return to Japan after just one season in Qatar
The deal marks the 29-year-old's second stint in Japan after accumulating more than 100 goals in over 200 appearances for Albirex Niigata and Urawa Reds between 2004 and 2011.
Edmilson also scored 26 goals from 49 appearances in domestic cup tournaments, but he could only net four times in 10 appearances for Al-Gharafa last season.
"I'm happy to have returned to Japan," the player said in an official club statement. "I'm grateful to FC Tokyo for giving me the opportunity and want to play as hard as I can for them."
Tokyo are currently in seventh place after 18 matches, with 28 points to their name, but have scored just 21 goals and suffered injuries to many first-team players.
As the third foreign player on the club's roster, the Brazilian will join countryman Lucas and South Korea international Jang Hyun-Soo.
Edmilson, who will wear the No.9 jersey, is expected to debut against his former club when Tokyo host Albirex Niigata on July 28.