Guatemalans Comunicaciones joined America on seven points in Group Eight after their victory in Puerto Rico.
Jose Contreras scored with an 18th-minute free-kick and William Coito's men sealed their win when Steven Estrada diverted a cross into his own net late on.
Both teams had a man sent off as Bayamon defender Alexis Rivera saw red late in the first half and Contreras was given his marching orders shortly after the break.
It sets up a winner-takes-all final match against Liga MX side America, who are top of the group, on October 21.
Alajuelense climbed to the top of Group Six despite being held to a 1-1 draw by Chorrillo in Panama.
The Costa Rican visitors took the lead through Kenner Gutierrez, but his goal was cancelled out by Sergio Moreno in the first half.
It saw Alajuelense go a point ahead of Cruz Azul, while Chorrillo are eliminated having played all four of their group matches.
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