The Mustangs (13-19) lost nine of their last 11 regular-season games before winning three straight in Anaheim to earn the school's first NCAA tournament bid.
Freshman guard Ridge Shipley was the hero as he sank the game-winning three-pointer with 13 seconds left.
Northridge thought it had taken the lead back with 4.6 seconds left, but forward Tre Hale-Edmerson was called for a charging foul on a made basket.
Northridge quickly fouled Poly guard Kyle Odister, who made his first free throw but missed his second.
Northridge forward J.J. Thomas grabbed the rebound with about three seconds left but the clock expired before he could get off a final shot.
Chris Eversley led Cal Poly with 18 points and was named the tournament's most valuable player. David Nwaba scored 17 and Shipley finished with 14.
The players led a postgame celebration that was clad in Poly green.
They didn't play "One Shining Moment" at the end of game but could have piped in Frank Sinatra singing "grab your coat and get your hat."
Earning an NCAA bid is great, but now come the frequent-flier miles.
The Big West champion was headed to the "play-in" game in Dayton, Ohio, on Tuesday or Wednesday, as soon the Poly-Northridge matchup was official.
The concept of allowing most teams to compete for the NCAA title produces excitement, upsets and sometimes a conference championship game featuring schools with a combined record of 29-36.
In the NCAA's expanded format, that means sometimes letting in teams with losing records.
Cal State Northridge (which finished 17-18) gave it a good run and the "Matadors" may be remembered as the "Midnight Ramblers" after pulling off successive upsets well after East Coast midnight.
Thursday, Northridge won a thrilling 87-84 overtime verdict over No. 4 Hawaii. Few people noticed because the game ended at 10:56 PDT.
A day later, night-watch Northridge did it again, taking down No. 3 Long Beach, 82-77, in another thriller that ended at 11:17 p.m.
"Everywhere we go we're the underdog," first-year Northridge Coach Reggie Theus said after Friday's win. "Everywhere we go people are picking the other team. I think that's good for us."
Not so fast, Reggie . . .
Coffee-addled NCAA bracket experts, surely considering only the win-loss records, predicted a Northridge win even though Cal Poly had defeated the Matadors four straight times entering Saturday's game.