Santa Clara's record is so bad (3-13-1) that even a win might not have saved the Toreros. And USD has to take Santa Clara's record as 2-13-1, since you don't count any games between the two in the formula. On top of all that, losing at Santa Clara carried with it a penalty. USD's SOS dropped from .5402 to .5205 in one fell swoop. USD's winning percentage is now .5294, instead of .5882 if they had won. I estimate a win would have still dropped their RPI to around 41...below the current cut line of 37/38.
Santa Clara has an awful winning percentage so a loss to them really dings you. EDIT: Never mind, Dan explained it far better than I.