Trailing by as many as a dozen points in the second half, Santa Clara (18-8, 5-6) got within five on three straight 3-pointers with six minutes to go but could not get over the hump.
San Francisco (17-10, 6-6) had an answer after each time, pushing the lead out to double digits before settling for the nine-point win and sweep in the season series.
Jamaree Bouyea scored a game-high 17 points to lead four players in double figures for San Francisco. Jimbo Lull scored 16 and pulled down a game-high 14 rebounds while Charles Minlend added 11 points and 10 boards to help give the Dons a 41-35 rebounding edge.
The Dons took advantage by holding a 12-3 edge in second chance points.
DJ Mitchell also had a double-double with 12 points and 10 rebounds while Jaden Bediako finished with a team-high 14 points for the Broncos who dropped their third straight at home after winning 17 in a row.
San Francisco used a 20-3 run to close out the opening half, holding the Broncos without a field goal for the final eight minutes, to turn an eight-point deficit into a 36-27 lead. Ryuny and Lull combined to score 11 points during the stretch.
The Broncos could not recover in the second half as the Dons maintained at least a nine-point lead until Keshawn Justice drained a 3-pointer, the first points beyond the arc for the Broncos, with just over eight minutes left in the game to pull within six.
Justice finished with four 3-pointers and 12 points, all in the second half, but it was too late for the Broncos who lost 80-61 at San Francisco on Jan. 9.
Santa Clara went without a field goal for a stretch of 10:59 of action. Bediako made a basket with 8:03 left in the opening half. Mitchell's turnaround jumper with 17:04 remaining in the game snapped the dry spell. The Broncos missed 10 straight field goals in that stretch.
Bouyea had seven assists and just one turnover in the game. Lull recorded his fourth double-double of season.
• The series began in 1908 and the Broncos hold a 116-111 lead. The 227 meetings are tied for the most against any Santa Clara opponent (227 vs. Saint Mary's). They Dons have now won five of the last nine meetings in Leavey Center.
• Guglielmo Caruso saw his first action since December. He checked into the game with 12:02 left in the first half and the Broncos leading 16-12. He played just five minutes, all in the first half. It marked his first action since Dec. 29 against Alcorn State. He missed last 10 games with lower right leg injury.
• Jaden Bediako hit double figures in scoring for the third straight game.
• DJ Mitchell had his second career double-double. He had 14 points and 10 rebounds vs. Notre Dame de Namur on Nov. 19.
The Broncos play Saturday at home against Loyola Marymount. Tipoff is set for 2 p.m.