Trinidad & Tobago teenager Kendall Jagdeosingh pulled the Islanders level in the 87th minute and Englishman Taiwo Atieno scored the winner two minutes later to give the Islanders the 3-2 aggregate victory.
The match started an hour late as the Juan Ramon Loubriel Stadium field needed to be drained because of heavy rain caused by Tropical Storm Hannah. It took Alajuela only five minutes to take the lead on a goal by Ariel Rodriguez.
The Islanders, tied for first in the USL First Division, join the Montreal Impact in the group stage.
D.C. United (USA)
Saprissa (Costa Rica)
Cruz Azul (Mexico)
Houston Dynamo (USA)
Luis Angel Firpo (El Salvador)
Jalapa (Guatemala) or San Francisco FC (Panama)
Harbour View (Jamaica) or UNAM (Mexico)
Joe Public (Trin. & Tobago)
Montreal Impact (Canada)
Puerto Rico Islanders
Tauro FC (Panama)