Crickett Williams scored 19 points for the Spartans (4-5), who lost to the Broncos (7-4) for the 12th consecutive time. Tatiana Taylor had 10 points and 13 rebounds.
Down by nine points in the first half and down 25-24 at halftime, the Broncos took control in the second half.
Thomas' three-pointer was part of a 9-0 run that gave the Broncos a 45-33 edge with 10 minutes remaining.
Two layups by Jessica Kellogg pulled San Jose State to within four with 48.6 seconds remaining, but the Spartans turned the ball over on their next possession and could get no closer.
Santa Clara has won 16 of the 19 games played in the series.