Queretaro's former Uruguay striker Carlos Bueno was brought down after 30 minutes and took the penalty himself, but saw his effort saved by goalkeeper Jonathan Orozco.
Just before half-time, midfielder Isaac Acuna was pushed by William Paredes for Queretaro's second spot-kick. Winger Hector Altamirano snatched the ball from Bueno's hands and put it on the spot but blasted the penalty over the bar.
Substitute Abraham Carreno put Monterrey ahead in the 48th minute and Luis Perez added their second with 16 minutes remaining.
Monterrey, winners of the Apertura title in December, are second in Group One of the Clausura, five points behind leaders Tigres UANL, who were held 0-0 at Guadalajara.
Earlier in the day, Pachuca's Argentine coach Pablo Marini resigned after his team fell to their fourth defeat in nine games, 1-0 away to Estudiantes UAG on Friday.
Marini, who leaves Pachuca bottom of Group Two, struggled to build a successful team in his six months at the helm, which included a poor fifth place at the Club World Cup in Abu Dhabi.
"Things did not work out as we had hoped. I had incredible support until today," he told reporters.
"One has to be sincere, honest and professional, taking the decision at the right time, unfortunately at the best club where I've been a trainer and where things didn't go well for me."
America lead Group Two after a 3-2 away win over Santos Laguna with two goals from midfielder Angel Reyna including their 88th-minute winner.
Pumas UNAM held a three-point lead over Cruz Azul and Morelia in Group Three before playing at Atlante later on Saturday.
The top two in each of the three groups and the two next best-placed teams in the overall standings after the 17-match round robin phase qualify for the quarter-finals.
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