In singles, Harvard also secured three quarterfinal berths in the first day.
Junior William Lee won his opening match and then eliminated Quaker captain Eric Szobotka, 6-5, 6-4, in the round of 16. However, Lee was defeated by freshman teammate Nguyen, 6-3, 6-2, in the quarterfinals.
Choo and Nguyen, who also won their opening round matches, came within one tiebreak each of reaching the singles finals. However, they were ousted by Columbia's Oscar Chow and Pavel Jefferson in the semis.
Choo upset No. 3 Ryan Harwood of Penn, 4-6, 6-5 (7-3), 6-2, in the quarterfinals, but fell to unseeded Jefferson, 6-3, 6-5 (7-2), in the semis.
Nguyen, after defeating Lee, was edged out in the semis, 2-6, 6-2, 6-5(7-1) by Chow.
"This was a great learning weekend for us," said Harvard Assistant Coach Peter Mandeau. "Since this is a young team, each opportunity to gain experience helps us build towards the future."