Jonathan McDonald scored with a 27th minute header, with the referee ignoring protests from Motagua players who claimed he was offside.
Alajuelense moves to 12 points, three ahead of Mexico's Morelia and Los Angeles Galaxy, which both have nine.
Luis Lopez had Motagua's only real chance in the 57th, but struck his shot straight at the Alajuelense goalkeeper.
Alajuelense dominated possession against a second string Motagua, which has lost all five of its games in the tournament.
On Wednesday in Group A, Los Angeles Galaxy defeated Mexico's Morelia 2-1. Morelia hosts Alajuelense on Oct. 18 and Motagua plays the Galaxy on Oct. 20 in the final games in the group.
In matches played on Tuesday and Wednesday, Mexico's Santos Laguna and Seattle Sounders qualified for the last eight of the competition.
The final round of matches in the group stage are held on Oct. 18, 19 and 20.