Mexico defender Carlos Salcido was hit by one of the water-filled bottles though not badly hurt as security officials were slow to react to the attack.
Inside the stadium, Tigres were given a better reception by their hosts as the Cruz Azul players formed a guard of honour to welcome the champions onto the field to loudspeakers blaring out the message: "At Cruz Azul we know how to show recognition. Best wishes champion Tigres."
Tigres were the better side and would have won but for some brilliant saves by 'Blue Machine' goalkeeper Jesus Corona. Lobos and Chilean Hector Mancilla also fired shots against the bar.
Atlante's new Ecuadorean signing Michael Arroyo scored the only goal a minute before half-time, tapping in a pass from Peruvian Andres Mendoza. Guadalajara had defender Patricio Araujo sent off in the dying minutes.
America were the only one of Mexico's three big clubs to taste victory. Ecuador striker Cristian Benitez made up for a first-half penalty miss by scoring the opening goal in the 70th minute of a 2-0 win at Queretaro.
Benitez's substitute Juan Medina scored the second in added-time as America, having revamped their management staff in a bid to recover from their abysmal form in the Apertura in the first half of the season, gave new coach Miguel Herrera a winning start.
