Eugene Phelps had 13 points and 10 rebounds, and T.J Robinson 12 points and 13 rebounds for the 49ers (4-4).
Tsung-Hsien Chang scored 32 points and Corey Chase added 14 for BYU-Hawaii (3-2).
Long Beach State led 82-66 before the Seasiders made it interesting late. Chang and Chase keyed a run of 12 straight points to cut the deficit to four with 1:57 remaining, but BYU-Hawaii got no closer.
Marques Whippy had 12 rebounds for the Seasiders.