The reigning premiers managed to turn a first innings defeat into an outright victory at Hillcrest Oval.
Resuming at 2-21, the Centurions were rolled for just 103 chasing 191, with Josh Inglis unbeaten on 61.
But the visitors retained a positive attitude despite the first innings loss, disposing of the Bears in their second innings for just 59.
Leg spinner Ty Hopes found his best form of the season, taking 5-16.
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READ NOWAs a result, Joondalup required 147 for victory from 30 overs for an unlikely win.
WA rookie Jaron Morgan guided the side home with 81 from 87 balls to complete a famous triumph by five wickets in the 29th over.
Joondalup faces Mt Lawley at Iluka this weekend.