Sunday's victory gave Atlante, which had not won a title in 14 years, a 2-1 win on aggregate over Pumas.
Clemente Ovalle scored with five minutes left to clinch the victory in a wild finish to the final series. Venezuelan international Giancarlo Maldonado gave Atlante the lead in the 59th minute, but Ismael Iniguez equalized for Pumas 10 minutes later.
Atlante was the second team to leave Mexico City in recent years because of poor fan support. Necaxa was lured to the city of Aguascalientes. Only three First Division teams are left in Mexico City: Club America, UNAM and Cruz Azul.
"This is for all the Atlante fans who had gone a long time without having a reason to celebrate," said Atlante coach Jose Guadalupe Cruz. "Maybe we weren't brilliant, but it is a reward to consistency. We faced adversity, but we beat it and now we have a crown."