The Atlante-Cruz Azul final marks the third time in four seasons that a pair of Mexican clubs will meet for the Concacaf crown.
Atlante, formerly based in Mexico City, won its only Concacaf title in 1983. Cruz Azul has won five Concacaf championships: 1969, 1970, 1971, 1996, 199
The goal was Marquez Lugo's second goal of the game and came after an eventful first half during which he had a goal disallowed and hit the crossbar before putting Atlante late in the half after being set up by Fernando Navarro.
Santos looked to be headed to its first Concacaf final when Argentine-Mexican Matias Vuoso evened the score in the 68th minute, but Venezuelan Giancarlo Maldonado put Atlante back ahead and even on aggregate six minutes later.
The game was marred by a late-game melee that resulted in red cards for Juan Pablo Rodriguez of Santos and Maldonado.
Cruz Azul will host the first leg of the title series on April 22; the second leg will be played in Cancun a week later.