Reigning champions Adelaide Strikers booked a play-offs spot of their own - also with three games remaining - with a seven-wicket win over the Sydney Sixers, whose loss in North Sydney leaves them in need of a miracle to qualify.
The Thunder were dominant almost from the outset of Saturday's first game, restricting Perth to their lowest total of the summer (8-116) after Lauren Smith (2-12) broke their star opening partnership.
The spinner trapped Beth Mooney (26) lbw as she misplayed a pull-shot to send the Australian representative packing for the first time in four innings and trigger a collapse of 7-35.
In a true team bowling performance, the tweakers found particular success, with Sam Bates (1-6) setting a record for fewest runs conceded bowling four overs in a WBBL match.
Only a late cameo from Amy Jones (37) saved the Scorchers from absolute disaster. The English international belted six boundaries from the final three overs to beef the score up a little.
In reply, Sri Lankan import Athapaththu almost single-handedly hoisted her side to a big victory, steadying the ship after the early loss of Phoebe Litchfield (8) and top-scoring with an unbeaten 77.
She belted 13 boundaries on her way to her second-highest total of the summer and now has 451 runs for the tournament. Her previous best result for a WBBL campaign was 182.
Heather Knight's side chased the total down with 23 balls remaining.
It's been quite the turnaround for the Thunder who finished on the bottom of the ladder last summer with only one win from 11 starts.
The Sixers were left to rue a similar batting collapse in the second game that opened the door for opener Katie Mack (45 off 37) to help guide the Strikers to a comfortable victory.
Star all-rounder Ellyse Perry (37) had the hosts off to a fast start but when her opening partner Suzie Bates was caught at fine leg from Tahlia McGrath's bowling, the Sixers slammed on the breaks.
McGrath (2-21) had Perry out in her next over during a top-order collapse of 4-32 that helped consign the hosts to 8-122.
Other than Perry, South African all-rounder Chloe Tryon (39) was the only Sixer to make double figures with the bat.
The Strikers never looked at risk of bottling the chase but were patient, only closing in on victory when Bridget Patterson (20) slapped Perry for three fours in the space of four balls during the 14th over.
McGrath was steady with 38 from 35 balls and hit the winning runs for four past third man to get the Strikers (3-124) home with 15 balls to spare.
Saturday's results open enough of a gap between the Thunder and Strikers and fifth-placed Sixers that they cannot be ousted from the top four.
The only way the Sixers can qualify for the finals from here is to win their remaining two games and hope the Brisbane Heat lose their final three, ideally all by big margins to boost their net run rate.
If not, the fourth-placed Heat will join the Strikers, Thunder and Scorchers in the final series that begins on November 28.
