The loss sent Wanneroo down to 14th, cancelling out the mathematical, but unlikely, chance the side had of making the finals.
The Roos had a day’s play to chase an achievable 250 for victory, but lost the match by 30 runs, falling for 219 in the 73rd over at Kingsway.
The hosts’ Jake Fawcett, who took five wickets on day one, completed an outstanding match with an unbeaten knock of 88 to save his side from embarrassment.
Outside of Fawcett, only Chris Quelch (32) and Josh Quelch (44) scored more than 30 in a line-up where eight batsmen scored just 12 or less.
Will Bosisto (4-88) and Sean Stuart (4-46) were the best of 10th-placed University’s bowlers.
Wanneroo’s final match of the season begins on Saturday when it faces 6th-placed Fremantle.