Needing 201 for victory, WA were struggling at 8-161 early on Sunday when Fanning limped his way to the crease nursing the hamstring injury which had put him on crutches just a day earlier.
Normally an opener, Fanning's makeshift role at No.10 was intended to support in-form skipper Aaron Hardie, who had already reached his half-century and held the key to WA's chances.
Fanning's injury was so bad that the only way the 25-year-old could scurry through for singles was via a hurried crab walk, almost resulting in a number of run-outs.
It proved enough though, with Fanning (14no off 82 balls) and Hardie (80no off 128 balls) lifting WA to victory in coach Beau Casson's first Shield game in charge.
Hardie shared a long hug with Fanning after his injured teammate hit a shot through the offside and crab walked his way through for the two winning runs.
The man-of-the-match honours went to Hardie, who held the second innings together as wickets tumbled around him.
In a match full of twists and turns, WA were rolled for 175 in their first innings in reply to Queensland's 307.
But WA paceman Jhye Richardson turned the game on its head when he snared 5-19 to roll the Bulls for 68 in their second dig.
WA entered day four at 5-134 and needing 67 more runs for victory, but they added just one run to their overnight score before suffering a double disaster.
Joel Paris was the first to fall on Sunday when he edged paceman Xavier Bartlett (4-53) behind.
Richardson departed for a duck next ball when his late attempt to leave a rising Bartlett delivery only resulted in the ball coming off the face of his bat and flying to slip.
Kieran Elliott (20 off 27 balls) helped steady the ship before becoming Bartlett's third victim of the morning, leaving WA needing 40 more runs and with just two wickets in hand.
It meant Fanning limped to the crease with everything on the line, and he produced the bravest display of his Shield career to lift WA to a famous win.
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