The win was breather for the 49ers (6-10), who dropped six straight games - including four to ranked opponents - in a rugged road trip to prep for its Big West opener at UC Irvine Thursday.
Fresno Pacific was held to 13 of 49 shooting, made four 3-pointers and was outrebounded 41-32.
Gabe Solarin scored 12 for the Sunbirds (5-7), with Madison Higgins adding 11 and Jeff Amazan 10.
Samuels made 7 of 10 field goals, including 2-for-2 on 3-pointers, and blocked two shots while Branford shot 6 of 9 from the field, including a pair of 3-pointers.
Long Beach State opened the second half on a 20-6 run, capped by a Samuels dunk. Fresno Pacific is 2-12 against D I foes since 2007.