Many of Pondexter's baskets came just when the Scarlet Knights (4-0) need them to turn back a Spartan surge. But her biggest was a 3-pointer, which came with 7:03 left in the game and Rutgers trailing 53-52.
With a defender in her face, Pondexter sank it deep from the right baseline, triggering a 14-2 run that shut the door on the Spartans' upset hopes.
Rutgers advances to the championship game against the winner of Vermont and Iowa, the tournament host.
The Scarlet Knights had three other players in double figures, shot 45 percent and forced 17 Spartan turnovers.
Matee Ajavon had 15 points and Essence Carson and Michelle Campbell each added 10.
San Jose State (2-2) stayed close through much of the game.
Six times in the second half, the Spartans either tied the score or cut the lead to fewer than three points before Rutgers pulled away in the final seven minutes.
After being held to one point in the first half, Lamisha Augustine found her touch in the second half to finish with 18 points, including 10-of-13 from the free throw line. Amber Jackson scored 13 points and Alisha Hicks chipped in 10.
San Jose shot 41 percent from the field, but shot hit just 29 percent of its 3-pointers.
Rutgers seemed in control early, as Pondexter scored eight early points in building a 13-4 lead five minutes into the game. Twice the Scarlet Knights held leads of 11 points, the second coming when Michelle Campbell scored inside to put Rutgers up 19-8 with 12:56 to go.
But the Spartans refused to back down. A lay-up by Jackson set off a 16-8 run, capped on the other end by Anetero Uiagalelei's 3-pointer that made the score 27-24.
A pair of free throws by Breana Fields with six seconds left in the half brought San Jose to within one point. But Pondexter, who had 14 first-half points, grabbed the inbound pass, drove the length of the floor and sank a pull-up jumper before the buzzer to give Rutgers a 37-34 lead at the break.