The result tied the two-game final at 2-2 on aggregate, giving Pachuca its third title in four years with more away goals.
"It's off the charts," sporting director Andres Fassi said, "to win a game like this. It's more energy for a club already full of passion."
Cruz Azul won the first leg 2-1 in its stadium in Mexico City.
Benitez scored on a bouncing shot that got past Cruz Azul goalkeeper Jesus Corona.
"I asked God to let me have the ball in front of the goal, and it was the last play," Benitez said. "I turned and when it went in I couldn't believe it."
The victory puts Pachuca into the Club World Cup later this year, as the top team in the Caribbean, North America and Central America region.
American midfielder Jose Francisco Torres, vying for a place on the U.S World Cup roster, started and played until the 80th minute for Pachuca.
Pachuca pressed hard in the final 10 minutes, forcing Corona to come up with several key saves before he was finally beaten by the Paraguayan striker from the left side.
Cruz Azul, lost last year's CONCACAF final to Mexican club Atlante. The club also lost three Mexican league finals in recent seasons, and was eliminated last weekend from this season's Mexican league playoffs.
Cruz Azul coach Enrique Meza, who coached Pachuca to two of its CONCACAF titles, joined Cruz Azul this season.
Meza also coached Pachuca to the Copa Sudamericana title in 2006, the only time a Mexican team won one of South America's top club tournaments.