Perth Scorchers needed three runs to win off the final delivery of the day, and although Mathilda Carmichael struck the Nicola Carey delivery well, she was found just short of her crease as she desperately scampered back for a second run.
As a result, Carmichael was run-out and the game ended in thrilling fashion.
Had she had made her ground, it would have been the second Rebel WBBL Super Over in the space of less than a week, following on from the Melbourne Renegades and Sydney Sixers at Geelong.
But the Thunder successfully defended their 6-145 and maintained top spot on the WBBL table, with Scorchers stranded on 6-144 at the end of their 20 overs.
The Scorchers claimed an early mini-victory, removing the in-form Rachael Haynes for just one run, but opening partner Rachel Priest made the most of the extra lives she was given after mishaps in the field, powering to 42, before her luck run out and she was caught by Villani off Nicole Bolton's bowling.
Piepa Cleary was the pick of the Scorchers' bowlers, claiming three wickets for 19 runs off three overs, while Bolton's brilliant form with the ball continued, taking 2-14 off four runs.
Taneale Peschel was the only other wicket-taker, finishing with figures of 1-19 (2).
Bolton continued her fine form with the bat, scoring her highest WBBL total in the competition's history, with 71 off 57 deliveries, including seven fours and one six. Her innings was eventually cut short, falling victim to a ball from Player-of-the-Match Rene Farrell.
The Thunder and Scorchers face each other for the second time tomorrow at 1.30pm WST at #TheFurnace. The game is followed by the KFC Big Bash League match where the Scorchers take on the Melbourne Renegades.