Goals by Carlos Esquivel and Brazilian-born Mexico international Antonio Naelson gave Group One leaders Toluca the victory which could have been bigger but for a penalty save by Queretaro's Argentine goalkeeper Carlos Bossio from Chilean Hector Mancilla.
The top two teams in the three groups plus the two best placed teams in the overall standings qualify for the quarter-finals.
Morelia edged closer to qualification with a 3-1 win over Guadalajara to consolidate their position at the top of Group Two.
Guadalajara owner Jorge Vergara did not hide his disappointment at his team's cautious game despite having appointed Raul Arias, a coach renowned for his pragmatic tactics, in September to get the team out of a slump.
"The truth is I don't like it, I like attacking football...I also understand we had to strengthen the back to stop conceding goals," said Vergara, who vowed when he bought the club in 2002 to make them the best in the world.
Guadalajara, one of Mexico's two most popular clubs, had taken five points from seven games when Arias took charge. After taking 10 points from their next seven matches, they are in danger of missing out on the quarter-finals.
VILLA GOALS
Cruz Azul, second in Group Three, beat Atlante 3-1 on Saturday with two goals by Argentine striker Emanuel Villa, who took his top marksman's tally to 13.
Group Three leaders Santos Laguna bade farewell to their Corona stadium with a 1-1 draw against title holders Pumas UNAM, who are bottom of the group.
The club from northern Mexico who have won three league titles including last year's Clausura, are moving to a brand new complex called "Santos Model Territory" to be inaugurated on November 11 against Santos of Brazil with Pele and FIFA president Sepp Blatter as guests of honour.
The complex includes the 30,000 capacity New Corona Stadium, a hotel overlooking the ground, a university, a shopping zone and a church.
The last goal scored at the Corona was Argentine-born striker Matias Vuoso's equaliser for Santos.
