Tigres defender Hugo Ayala was shown his second yellow card and sent off three minutes later, but a solo effort from Alan Pulido in the 58th leveled the scores and brought Tigres to within one goal of victory.
Cruz Azul needed to win by three goals to have a chance of progressing and took the lead through a Christian Gimenez penalty in the 33rd, but Toluca equalized via Paraguayan Pablo Velazquez in the 78th.
Jair Pereira was sent off for Cruz Azul in second half injury time for a foul inside the penalty area, with Toluca's goalkeeper Alfredo Talavera stepping up to take it and blasting the shot over the bar.
Colombia's Darwin Quintero scored twice in the last 25 minutes to take the game beyond Queretaro.
Dario Burbano, also of Colombia, struck into the top right corner from outside the penalty area to open the scoring for Leon in the 28th. Mauro Boselli, Matias Britos and Jose Juan Vazquez added second half goals for Leon, with Morelia taking risks in order to get back into the tie.