After losing her superstar opening partner Sophie Devine (4) early, Mooney (101no) almost single-handedly steered the Scorchers to a competitive 4-159 at the Junction Oval on Sunday.
In reply, the resurgent Thunder fell to 3-18 by the end of the powerplay, having not dropped any wickets there in their previous seven games.
Young quick Chloe Ainsworth (2-8) set the carnage in motion by snaring the wickets of Chamari Athapaththu (10) and Marizanne Kapp (0) in consecutive balls.
Australian representative Phoebe Litchfield (45) offered resistance at first drop but was caught in the deep from Amy Edgar's bowling (3-18) before the Thunder sputtered to 8-117.
The loss was only the second of the tournament for the Thunder and relegated them to second spot on the ladder behind the Scorchers, who have won five of their last six games.
It took until the twilight of the Scorchers' innings for Mooney to enjoy a steady partnership as in-form Hannah Darlington (2-26) spearheaded the Thunder attack to silence her Perth teammates.
Chloe Piparo (22no from 16 balls) did well to help Mooney steady the ship following the loss of Amy Jones (7) just as Perth looked primed to take the power surge.
Mooney had played a patient innings but smacked Sammy-Jo Johnson for four fours from five deliveries in the final over to snatch the ascendancy for the Scorchers.
On 97, Mooney pulled stand-in Thunder captain Johnson past deep mid-wicket for four to bring up an unbeaten third WBBL ton on the last ball of the innings and the 61st delivery she faced.
Mooney is now the only player to have passed 400 total runs in all nine iterations of the WBBL and is the current edition's second-highest run-scorer, only one run behind Devine.
"That's the hallmark of Beth Mooney, she's ultra-consistent. That's her biggest strength," Piparo said.
"She's all class at the top of the order."
The Melbourne Renegades appear at serious risk of claiming their second wooden spoon after a four-run loss to rivals the Melbourne Stars that went down to the final over.
Annabel Sutherland (4-22) dispatched Hayley Matthews (32) and Sarah Coyte (0) in consecutive balls in the 18th over to swing the momentum of see-sawing contest squarely into the Stars' favour.
The quick earlier bowled Tammy Beaumount (33) and had Harmanpreet Kaur (37) caught behind after both internationals got a start on the road to 145 for victory.
Jess Duffin (5no) needed a six from the last ball of the final Sasha Moloney over to snatch a win that had looked likely at the mid-point of the Renegades innings.
But she could not find the rope past long off and the Stars held on as the Renegades finished at 6-140.
There is now a four-point gap between the seventh-placed Stars and the Renegades, who likely need to win at least two of their last four games to climb from the bottom of the ladder.
They have won only one of 10 matches this summer.
Annabel Sutherland claimed 4-22 as the Melbourne Stars defeated the Melbourne Renegades in the WBBL.
Earlier, Meg Lanning (67no) led the Stars to 5-144 in her second knock since announcing her international retirement on Thursday.
Dropped on 42, Lanning brought up her third half-century of the WBBL summer with a single to backward square leg in the 18th over.
But losing partner Sophie Reid in the final over scuppered her hopes of beefing the total up any further.
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