Jonathan McDonald scored on a header in the 27th minute as the referee ignored protests from Motagua players who claimed he was offside.
Alajuelense now has 12 points, three ahead of Mexico's Morelia and the Los Angeles Galaxy.
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 is 0-5 in the tournament.
On Wednesday in Group A, the 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.
Also, Mexico's Santos Laguna and the Seattle Sounders qualified for the last eight of the competition.
The final round of matches in the group stage will be held Oct. 18-20.