Luis Tena's men trailed 2-0 courtesy of an Enner Valencia brace midway through the second half at the Estadio Azul.
Valencia's first goal was a tap-in to an empty net, after Cruz Azul shot-stopper Guillermo Allison completely misjudged a through ball - and to make matters worse, embarrassingly crashed into his own defender Horacio Cervantes as the Ecuadorian scored the opener.
The former Emelec man doubled his tally in the 62nd minute, after a classy cut-back pass from substitute Hirving Lozano found the forward, who tucked away his shot.
Cruz Azul battled on, however, as Christian Gimenez scored after Pachuca custodian Oscar Perez saved his spot kick.
And in the first minute of injury time, American Michael Farfan - who only came on after 80 minutes - scored the winner.
Tena's two substitutes for the game combined for the equaliser, as Cameroon international Achille Emana's powerful shot was parried by Perez into the path of Farfan, who tucked away the all-important goal via his left boot.
The point ensured Cruz Azul still have a two-point lead at the top, although Toluca are within striking distance after their 2-1 home win over Leon.
Toluca had to come from behind after Ivan Pineda gave the visitors a 19th-minute lead.
But a drought-breaking win would not eventuate for Leon, now without a league victory in six, as Toluca stormed to victory via goals from Gabriel Velasco and Oscar Rojas.
Nine and 10 points off the pace respectively, Santos Laguna (third) and America (fourth) both recorded wins.
Carlos Quintero scored a hat-trick for Santos as they staved off an ever-resilient Atlante 4-3 at home, while America had a 1-0 win at bottom club Puebla courtesy of Miguel Layun's second-minute strike.
Pumas UNAM are fifth on 22 points, one behind America, after coming from behind to earn a 1-1 draw at Veracruz.
Tijuana struck late-on via Richard Ruiz, as they earned a point in a 1-1 stalemate at Tigres UANL.
Strugglers Chiapas and Monterrey shared the spoils 1-1 in their clash, while Guadalajara were held at home by Morelia in a 1-1 result.
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