Johnny Dee led the Toreros with 25 points, and made some huge 3-pointers in the second half to keep USD close or barely ahead.
But it was Dee's 3-point play with 2:12 remaining, a runner off the glass that drew a foul on Craig Cusick, that proved to be the biggest play of the game. It gave the Toreros a 65-62 lead after Brandon Davies tied it with a pair of free throws.
Down by three, the Cougars seemingly came up with a steal, but gave the ball right back and Chris Anderson hit a pair of free throws to give the Toreros a five-point lead that was too much for the Cougars to overcome.
Matt Carlino's 3-pointer with 6 seconds left cut it to one. After Dee made two free throws, Carlino's desperation 3-point attempt for the tie rimmed out and USD had its second-straight win over the Cougars.
Tyler Haws and Brandon Davies scored 20 points apiece for BYU and Carlino added 13.
Anderson had 16 for San Diego as BYU once again had trouble containing the Toreros' guards.
Trailing 35-28 at halftime, the Cougars roared out of the locker room after intermission looking like a different team than the one that was thoroughly outplayed in the first 20 minutes, and surged ahead 40-38 before the first media timeout.
Haws finally heated up for the Cougars after a dismal first half, and also got to the free-throw line consistently, but the Cougars quickly lost the lead just as fast as they got it. Dee's 3-pointer with 8:19 left gave the Toreros a 54-49 lead, but BYU rallied to go ahead with just under six minutes remaining.
Matt Carlino's 3-pointer gave BYU a 58-56 and momentarily got the pro-BYU crowd into the game, but Anderson matched the long-range shot moments later. Then Haws gave BYU a 60-59 lead, only to watch Dee hit another 3-pointer from the corner.
The Cougars led just once in the first half, 2-0, when Davies controlled the opening tip and then scored in the paint.
They tied it 11-11 on a Matt Carlino jumper, then quickly fell behind again, thanks to shoddy defense on USD's perimeter shooters.
Dee and Ken Rancifer had 10 points apiece in the first half for USD, with Rancifer hitting back-to-back 3-pointers to stretch the Toreros lead to 26-18 with 6:50 remaining in the half.
The Cougars missed four straight layups at one juncture of the first half. It was that kind of night for the WCC's third-place team.