Zane Johnson had 13 points for the Rainbow Warriors (5-4), who hosted a regular-season game on Maui for a second straight year.
Marc Hill had 17 points and DaMetrius Upchurch 11 for the Aggies (4-8).
Hawaii led 49-48 with 7:45 remaining when two free throws by Stokes ignited a 12-0 run over the next 4:22. Two Joaquim field goals and a three-point play by Stokes highlighted the surge.
Joaquim had seven rebounds.