Substitute Rodolfo Vilchis grabbed the winner four minutes from time as Queretaro built on their 1-0 victory over Morelia on the first matchday.
With Queretaro leading the division on six points, there are six teams in second position on four points including defending champions Leon, Cruz Azul, Guadalajara and Tijuana.
Leon continued their unbeaten start as they swept aside Atlas 3-1 with Carlos Pena securing a brace through strikes in the third and 38th minutes.
Luis Montes made it three on 77 minutes before Maikon Leite pulled a goal back for Atlas two minutes later.
Toluca twice came from behind to deny Morelia their first win as the sides drew 2-2.
It only took Toluca's Edgar Benitez two minutes to cancel out Carlos Morales' fifth-minute opener before Morelia re-took the lead through Christian Valdez in the shadows of half-time.
But Toluca again forced the equaliser on 56 minutes as Pablo Velazquez converted from the penalty spot.
Cristian Pellerano scored an 87th-minute winner as Tijuana stole a late 1-0 win over last season's beaten finalists America.
In other matches, 10-man Veracruz stunned Atlante 2-1, Puebla and Monterrey drew 1-1 and it was goalless between Tigres and Pachuca.
Guadalajara won 1-0 against Chiapas while Cruz Azul scored a 90th-minute winner in a 2-1 triumph over Santos Laguna.
