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."
The match ended 1-1 with both goals coming from Argentines. Christian Gimenez put Cruz Azul ahead with a superb free-kick into the top corner after seven minutes with fellow midfielder Lucas Lobos equalising in the 71st minute.
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.
Guadalajara, who were favourites for the Apertura title after topping the standings in the league phase before being upset by Queretaro in the quarter-finals, crashed to a 1-0 home defeat by Atlante at the Omnilife.
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.
Benitez could have put America ahead after half an hour at La Corregidora but he was ordered to retake the penalty for encroachment, having found the net, and his second effort was well saved by goalkeeper Liborio Sanchez.
The Ecuadorean made amends when he scored from a pass by fellow forward Matias Vuoso and shot across Sanchez inside the far post.
Queretaro were without Uruguayan striker Carlos Bueno, who top-scored for them in the Apertura but has moved to San Lorenzo in Argentina, and conceded the second when Medina netted a pass from Colombian central defender Aquivaldo Mosquera at a corner.
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