Atlante fire coach Cruz
Atlante, coached by Cruz since 2006, finished bottom of Group Three last weekend, missing out on the eight-team knockout phase for the title.
"Cycles come to an end and Prof. Cruz's has concluded with Atlante," club president Jose Antonio Garcia told Televisa.
"He's a great coach who did a lot for Atlante but we're going to have to find a new trainer."
Cruz steered Atlante, nicknamed the "Iron Colts", to the Apertura title in 2007 and the CONCACAF Champions League last year.
This earned them the right to play in the Club World Cup in Abu Dhabi in December where they finished fourth in the tournament won by Barcelona.