Pablo Velazquez and Raul Nava both scored twice for Toluca, with Atlante finishing the game with nine players.
Atlante's Luis Gerardo Venegas and Toluca's Carlos Rodriguez were sent off following a scuffle in the 32nd, and Atlante's Paul Uscanga picked up his second yellow card in second half injury time.
Paulo da Silva, Isaac Brizuela and Wilson Mathias got Toluca's other goals, with Ezequiel Miralles netting Atlante's only goal in the 47th.
The victory moved Toluca into third position.
Santos Laguna came from behind on Friday after Jose Maria Cardenas tapped in to give Morelia the lead in the 6th.
Rodolfo Salinas equalized four minutes later with a volley from the edge of the penalty box, with Oribe Peralta and Darwin Quintero adding the others before halftime.
Santos held on to the two-goal cushion despite playing the second half with 10 men after Mauro Cejas was sent off in first half injury time.
Pumas recorded their first win of the season and moved up from last place in the league, with former Liverpool player Luis Garcia pouncing in the 81st against Monterrey.