The hosts took the lead in the 34th minute, when Camilo Sanvezzo headed home a corner kick from Kevin Gutiérrez to make it 1-0.
Juárez pressed forward after falling behind, but Querétaro stood firm defensively, and it looked like the Gallos Blancos would hold on for victory by the minimum difference.
Then, in stoppage time, Mario Ortiz tied the game with a header of his own to send the match to a penalty shootout.
In the shootout, Raúl Enríquez, Josué Gómez, Eder Borelli, and Lucas Silva all scored for Juárez while Camilo Sanvezzo was the only Querétaro player to find the net.
FC Juárez advances to the quarterfinals with the 1-1 draw (4-1 shootout win) while Querétaro, the reigning champion, is eliminated.