With the Mustangs trailing by two and under 15 seconds remaining, Shipley sank a triple from the top of the key to put his squad on top.
Cal Poly sophomore Zach Gordon drew a charging foul against Tre Hale-Edmerson at the other end, but Kyle Odister split two free throws with 4.0 seconds left to leave the door open for Cal State Northridge.
However, the Matadors failed to get a desperation heave up before the final horn sounded, allowing Cal Poly to escape with its first Big West Conference tourney crown.
Chris Eversley supplied 18 points and Dave Nwaba added 17 points for the seventh-seeded Mustangs (13-19), who became the lowest seed in the 39-year history of the event to claim the championship.
Stephen Maxwell led Cal State Northridge (17-18) with 18 points, while Stephan Hicks contributed 11 points and 12 rebounds for the Matadors, who were looking to secure their third NCAA Tournament appearance and first since 2009.
Cal State Northridge led 49-45 with just under seven minutes to play, but Shipley reeled off six straight points to give Cal Poly a two-point edge.
The teams exchange buckets from there until a 6-0 surge from the Matadors gave them a 59-55 lead with just over 1 1/2 minutes left.
Early on, Cal State Northridge led 21-10 with 8:24 to play in the first half, but a quick 7-0 sprint brought the Mustangs to within four, which is where the margin stood as the teams entered the break.
Cal Poly opened the second stanza with six straight points and the teams went back-and-forth for the remainder of the contest.