Atlas became Mexican champions after 70 years of waiting thanks to the victory on penalties against Leon in the second leg of the championship.
At home, at the Jalisco stadium in Guadalajara, Atlas won 1-0 on a goal from their midfielder Aldo Rocha (55th).
Beaten 3-2 in the first leg, the Mexican club snatched extra time, then penalties.
On penalties, Atlas won 4-3 thanks to Colombian goalkeeper Camilo Vargas, who saved two shots.
Atlas, which won the second title in its history after that of the 1950-51 season, succeeds Cruz Azul, champion in the first half of 2021.