Chasing a DLS-adjusted target of 75 to win from a rain-reduced 16 overs, the Sydney Thunder were 2/28 in reply when rain stopped play, for the third time, after 5.3 overs of the chase.
The Sixers were dismissed for 76 in 15.5 overs at Sydney Showgrounds Stadium.
Justin Avendano top-scored with 28 from 31 deliveries. Thunder left-arm seamer Daniel Sams claimed 3-14.
Sixers seamer Jackson Bird returned 1-5 from the three overs he bowled.
Despite the loss, the Sixers remain second on the BBL|09 ladder, seven points behind Melbourne Stars.
The Stars are the Sixers next opponent at the SCG on Monday night.