Last season saw Alajuelense beaten 3-0 against Toluca over two legs in the final four of the competition.
And Alajuelense look set for another semi-final appearance thanks to Jose Ortiz and his two-goal haul against the MLS outfit at Estadio Alejandro Morera Soto.
United are still in pre-season, with the MLS set to kick-off next week, and it showed as Alajuelense raced to a two-goal lead thanks to Eithel Rodriguez and Ortiz.
Rodriguez made the breakthrough in the 16th minute via a penalty after Armando Rodriguez was brought down by United goalkeeper Andrew Dykstra, who received a yellow card.
Ortiz doubled the home side's lead five minutes later after being played in by Johan Venegas.
United were given some hope in the 23rd minute when Fabian Espindola headed past Dexter Lewis, though Alajuelense responded within three minutes courtesy of Venegas' tap in.
Ortiz netted his second of the match and made it 4-1 nine minutes into the second half after firing the ball low and hard beyond Dykstra.
Steve Birnbaum reduced the deficit two minutes from the end with a close-range header, only for Jonathan McDonald to restore the hosts' three-goal buffer 60 seconds later.
The return leg is scheduled for March 4 at Robert F. Kennedy Memorial Stadium in Washington.
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