After the Sixers struggled to cope with the low Spotless Stadium wicket to be held to just 7-98, Rachael Haynes and Naomi Stalenberg guided the home side to victory as they chased down the target with 14 balls to spare.
Haynes' 43 was her fourth straight score above 30 to underline her return to form, while Stalenberg made a composed unbeaten 44 from 50 balls.
The win lifted the Thunder to second on the ladder with four round games to play, one win behind the Sixers but with a match in hand.
The Sixers were earlier never really in the match after they fell to 6-33, with Lisa Griffith (2-24) taking the key wickets of Alyssa Healy (9) and Ellyse Perry (13) in the third over to start the rut.
Only Marizanne Kapp (40 not out) and Lauren Smith (22) gave the Sixers any real hope, as debutant Rachel Trenaman and Nicola Carey both also claimed two wickets for the hosts.