The Tritons held a 63-59 lead with 2:20 left in the second OT, but the Coyotes scored the final seven points of the game to escape with the win and spoil UCSD's home opener.
Tre' Brewer scored 15 points to lead four players in double figures for CSUSB (2-0 overall, 1-0 CCAA). Alexander finished with 14 points and 11 rebounds, while Theron Laudermill also tallied a double-double with 13 points and 13 boards. D. J. Shumpert added 11 points and six rebounds.
Tyler McGrath scored 15 points and grabbed seven rebounds to pace UCSD (3-2 overall, 0-1 CCAA), while Christian Hatch recorded his second straight double-double with 11 points and a career-high 15 rebounds. Justin Brue and Ryan Peters scored 10 points apiece.
After neither squad led by more than three in the first overtime period, the Tritons looked to have finally separated themselves after scoring six straight points early in the second OT. Brue hit a jumper that tied the game at 59 and, after a pair of free throws from James McCann, sank another from the free throw line that put UCSD on top by five with 2:20 left to play.
The Coyotes refused to roll over though, scoring the next three points at the foul line to pull within one with 1:19 remaining. After Dylan Bohanan's three-point try missed the mark on the Tritons' next possession, Alexander drove down the lane and scored to give the lead back to the visitors with 18 ticks on the clock.
Bohanan had another look on a long three on the ensuing trip, but his potential game-winner went halfway down and rimmed out and Shumpert corralled the rebound to seal the win for the Coyotes.
Neither team shot the ball particularly well, as San Bernardino finished at 41% (26-64) from the field and UCSD shot at a 35% (24-69) clip. The Coyotes hit just 3-of-19 from the three-point line, while the Tritons were 5-of-19.
McGrath finished 5-of-11 from the floor, including 3-of-8 from behind the arc, while Hatch was just 4-of-14 and Brue was 5-for-12. Peters converted four of his six attempts, finishing 2-of-3 on threes.
CSUSB had a slim 45-42 advantage on the glass and outscored UCSD 34-28 in the paint.
UCSD led 30-22 at halftime but the Coyotes outscored the Tritons 17-4 over the first seven minutes of the second half to take a 39-34 advantage. UCSD came back with the next five points to tie the game at 39 and neither team led by more than three for the rest of the period.
Both squads had an opportunity to seal the game in regulation, but Hatch missed a jumper for the Tritons and Laudermill came up empty for the Coyotes.
Tuesday's game marked UCSD's third double overtime contest in the past two seasons. UCSD defeated Cal State L.A. (76-73) and San Francisco State (87-82) in double OT in 2010-11.
The Tritons are off the rest of the week and will return to the court against CCAA rivals Cal State Dominguez Hills and Cal State L.A. on the road December 2-3.