Queretaro remain bottom of the Mexican Apertura after suffering their sixth defeat in seven games this season.
Esteban Paredes scored the only goal of the game after 17 minutes to give visitors Atlante all three points.
At the other end of the table, Leon moved into third place with a 2-0 win at San Luis, with Eisner Loboa and Matias Britos on target.
Cruz Azul dropped down to fourth after being held 1-1 at home to Pachuca, who took the lead through Felix Borja after 25 minutes. It took until the last minute for the home side to equalise courtesy of Gerardo Torrado.
Elsewhere, Santos Laguna beat Tigres Monterrey 3-1 with Carlos Quintero and Oribe Peralta putting the home side 2-0 up inside 16 minutes. Lucas Lobos pulled a goal back from the penalty spot on 37 minutes, but Quintero's second on 74 minutes sealed the win.
The day's other game saw Monterrey and Atlas draw 1-1. Neri Cardozo opened the scoring after just five minutes, but susbtitute Jahir Barraza scored within seconds of coming on to earn Atlas a point.